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        Module&nbsp;Spectrum_mod
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<h1 class="epydoc">Source Code for <a href="dadi.Spectrum_mod-module.html">Module dadi.Spectrum_mod</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">   1</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno">   2</tt>  <tt class="py-line"><tt class="py-docstring">Contains Spectrum object, which represents frequency spectra.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">   3</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno">   4</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">logging</tt> </tt>
<a name="L5"></a><tt class="py-lineno">   5</tt>  <tt class="py-line"><tt class="py-name">logging</tt><tt class="py-op">.</tt><tt class="py-name">basicConfig</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L6"></a><tt class="py-lineno">   6</tt>  <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable dadi.Hessian.logger=dadi.Hessian-module.html#logger,Variable dadi.Inference.logger=dadi.Inference-module.html#logger,Variable dadi.Integration.logger=dadi.Integration-module.html#logger,Variable dadi.Numerics.logger=dadi.Numerics-module.html#logger,Variable dadi.RunInParallel.logger=dadi.RunInParallel-module.html#logger,Variable dadi.Spectrum_mod.logger=dadi.Spectrum_mod-module.html#logger"><a title="dadi.Hessian.logger
dadi.Inference.logger
dadi.Integration.logger
dadi.Numerics.logger
dadi.RunInParallel.logger
dadi.Spectrum_mod.logger" class="py-name" href="#" onclick="return doclink('link-0', 'logger', 'link-0');">logger</a></tt> <tt class="py-op">=</tt> <tt class="py-name">logging</tt><tt class="py-op">.</tt><tt class="py-name">getLogger</tt><tt class="py-op">(</tt><tt class="py-string">'Spectrum_mod'</tt><tt class="py-op">)</tt> </tt>
<a name="L7"></a><tt class="py-lineno">   7</tt>  <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno">   8</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">operator</tt> </tt>
<a name="L9"></a><tt class="py-lineno">   9</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L10"></a><tt class="py-lineno">  10</tt>  <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno">  11</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L12"></a><tt class="py-lineno">  12</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">newaxis</tt> <tt class="py-keyword">as</tt> <tt class="py-name">nuax</tt> </tt>
<a name="L13"></a><tt class="py-lineno">  13</tt>  <tt class="py-line"><tt class="py-comment"># Account for difference in scipy installations.</tt> </tt>
<a name="L14"></a><tt class="py-lineno">  14</tt>  <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L15"></a><tt class="py-lineno">  15</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">misc</tt> <tt class="py-keyword">import</tt> <tt class="py-name">comb</tt> </tt>
<a name="L16"></a><tt class="py-lineno">  16</tt>  <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L17"></a><tt class="py-lineno">  17</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">comb</tt> </tt>
<a name="L18"></a><tt class="py-lineno">  18</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">integrate</tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Function dadi.Numerics.trapz()=dadi.Numerics-module.html#trapz"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-1', 'trapz', 'link-1');">trapz</a></tt> </tt>
<a name="L19"></a><tt class="py-lineno">  19</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">special</tt> <tt class="py-keyword">import</tt> <tt class="py-name">betainc</tt> </tt>
<a name="L20"></a><tt class="py-lineno">  20</tt>  <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno">  21</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Package dadi=dadi-module.html"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-2', 'dadi', 'link-2');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module dadi.Numerics=dadi.Numerics-module.html"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-3', 'Numerics', 'link-3');">Numerics</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno">  22</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-4', 'dadi', 'link-2');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-5', 'Numerics', 'link-3');">Numerics</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Function dadi.Numerics.reverse_array()=dadi.Numerics-module.html#reverse_array"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-6', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name" targets="Function dadi.Numerics._cached_projection()=dadi.Numerics-module.html#_cached_projection"><a title="dadi.Numerics._cached_projection" class="py-name" href="#" onclick="return doclink('link-7', '_cached_projection', 'link-7');">_cached_projection</a></tt><tt class="py-op">,</tt> <tt id="link-8" class="py-name" targets="Function dadi.Numerics._lncomb()=dadi.Numerics-module.html#_lncomb"><a title="dadi.Numerics._lncomb" class="py-name" href="#" onclick="return doclink('link-8', '_lncomb', 'link-8');">_lncomb</a></tt> </tt>
<a name="Spectrum"></a><div id="Spectrum-def"><a name="L23"></a><tt class="py-lineno">  23</tt>  <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno">  24</tt> <a class="py-toggle" href="#" id="Spectrum-toggle" onclick="return toggle('Spectrum');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html">Spectrum</a><tt class="py-op">(</tt><tt class="py-base-class">numpy</tt><tt class="py-op">.</tt><tt class="py-base-class">ma</tt><tt class="py-op">.</tt><tt class="py-base-class">masked_array</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="Spectrum-expanded"><a name="L25"></a><tt class="py-lineno">  25</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L26"></a><tt class="py-lineno">  26</tt>  <tt class="py-line"><tt class="py-docstring">    Represents a frequency spectrum.</tt> </tt>
<a name="L27"></a><tt class="py-lineno">  27</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno">  28</tt>  <tt class="py-line"><tt class="py-docstring">    Spectra are represented by masked arrays. The masking allows us to ignore</tt> </tt>
<a name="L29"></a><tt class="py-lineno">  29</tt>  <tt class="py-line"><tt class="py-docstring">    specific entries in the spectrum. Most often, these are the absent and fixed</tt> </tt>
<a name="L30"></a><tt class="py-lineno">  30</tt>  <tt class="py-line"><tt class="py-docstring">    categories.</tt> </tt>
<a name="L31"></a><tt class="py-lineno">  31</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L32"></a><tt class="py-lineno">  32</tt>  <tt class="py-line"><tt class="py-docstring">    The constructor has the format:</tt> </tt>
<a name="L33"></a><tt class="py-lineno">  33</tt>  <tt class="py-line"><tt class="py-docstring">        fs = dadi.Spectrum(data, mask, mask_corners, data_folded, check_folding,</tt> </tt>
<a name="L34"></a><tt class="py-lineno">  34</tt>  <tt class="py-line"><tt class="py-docstring">                           pop_ids, extrap_x)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">  35</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L36"></a><tt class="py-lineno">  36</tt>  <tt class="py-line"><tt class="py-docstring">        data: The frequency spectrum data</tt> </tt>
<a name="L37"></a><tt class="py-lineno">  37</tt>  <tt class="py-line"><tt class="py-docstring">        mask: An optional array of the same size as data. 'True' entires in</tt> </tt>
<a name="L38"></a><tt class="py-lineno">  38</tt>  <tt class="py-line"><tt class="py-docstring">              this array are masked in the Spectrum. These represent missing</tt> </tt>
<a name="L39"></a><tt class="py-lineno">  39</tt>  <tt class="py-line"><tt class="py-docstring">              data categories. (For example, you may not trust your singleton</tt> </tt>
<a name="L40"></a><tt class="py-lineno">  40</tt>  <tt class="py-line"><tt class="py-docstring">              SNP calling.)</tt> </tt>
<a name="L41"></a><tt class="py-lineno">  41</tt>  <tt class="py-line"><tt class="py-docstring">        mask_corners: If True (default), the 'observed in none' and 'observed </tt> </tt>
<a name="L42"></a><tt class="py-lineno">  42</tt>  <tt class="py-line"><tt class="py-docstring">                      in all' entries of the FS will be masked. Typically these</tt> </tt>
<a name="L43"></a><tt class="py-lineno">  43</tt>  <tt class="py-line"><tt class="py-docstring">                      entries are unobservable, and dadi cannot reliably</tt> </tt>
<a name="L44"></a><tt class="py-lineno">  44</tt>  <tt class="py-line"><tt class="py-docstring">                      calculate them, so you will almost always want</tt> </tt>
<a name="L45"></a><tt class="py-lineno">  45</tt>  <tt class="py-line"><tt class="py-docstring">                      mask_corners=True.g</tt> </tt>
<a name="L46"></a><tt class="py-lineno">  46</tt>  <tt class="py-line"><tt class="py-docstring">        data_folded: If True, it is assumed that the input data is folded. An</tt> </tt>
<a name="L47"></a><tt class="py-lineno">  47</tt>  <tt class="py-line"><tt class="py-docstring">                     error will be raised if the input data and mask are not</tt> </tt>
<a name="L48"></a><tt class="py-lineno">  48</tt>  <tt class="py-line"><tt class="py-docstring">                     consistent with a folded Spectrum.</tt> </tt>
<a name="L49"></a><tt class="py-lineno">  49</tt>  <tt class="py-line"><tt class="py-docstring">        check_folding: If True and data_folded=True, the data and mask will be</tt> </tt>
<a name="L50"></a><tt class="py-lineno">  50</tt>  <tt class="py-line"><tt class="py-docstring">                       checked to ensure they are consistent with a folded</tt> </tt>
<a name="L51"></a><tt class="py-lineno">  51</tt>  <tt class="py-line"><tt class="py-docstring">                       Spectrum. If they are not, a warning will be printed.</tt> </tt>
<a name="L52"></a><tt class="py-lineno">  52</tt>  <tt class="py-line"><tt class="py-docstring">        pop_ids: Optional list of strings containing the population labels.</tt> </tt>
<a name="L53"></a><tt class="py-lineno">  53</tt>  <tt class="py-line"><tt class="py-docstring">        extrap_x: Optional floating point value specifying x value to use</tt> </tt>
<a name="L54"></a><tt class="py-lineno">  54</tt>  <tt class="py-line"><tt class="py-docstring">                  for extrapolation.</tt> </tt>
<a name="L55"></a><tt class="py-lineno">  55</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="Spectrum.__new__"></a><div id="Spectrum.__new__-def"><a name="L56"></a><tt class="py-lineno">  56</tt> <a class="py-toggle" href="#" id="Spectrum.__new__-toggle" onclick="return toggle('Spectrum.__new__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#__new__">__new__</a><tt class="py-op">(</tt><tt class="py-param">subtype</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">mask</tt><tt class="py-op">=</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">nomask</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L57"></a><tt class="py-lineno">  57</tt>  <tt class="py-line">                <tt class="py-param">data_folded</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">check_folding</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-param">dtype</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-param">copy</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L58"></a><tt class="py-lineno">  58</tt>  <tt class="py-line">                <tt class="py-param">fill_value</tt><tt class="py-op">=</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">nan</tt><tt class="py-op">,</tt> <tt class="py-param">keep_mask</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-param">shrink</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L59"></a><tt class="py-lineno">  59</tt>  <tt class="py-line">                <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">extrap_x</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.__new__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.__new__-expanded"><a name="L60"></a><tt class="py-lineno">  60</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asanyarray</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno">  61</tt>  <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno">  62</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">mask</tt> <tt class="py-keyword">is</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">nomask</tt><tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno">  63</tt>  <tt class="py-line">            <tt class="py-name">mask</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">make_mask_none</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno">  64</tt>  <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno">  65</tt>  <tt class="py-line">        <tt class="py-name">subarr</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_array</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">mask</tt><tt class="py-op">,</tt> <tt class="py-name">dtype</tt><tt class="py-op">=</tt><tt class="py-name">dtype</tt><tt class="py-op">,</tt> <tt class="py-name">copy</tt><tt class="py-op">=</tt><tt class="py-name">copy</tt><tt class="py-op">,</tt> </tt>
<a name="L66"></a><tt class="py-lineno">  66</tt>  <tt class="py-line">                                       <tt class="py-name">fill_value</tt><tt class="py-op">=</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">nan</tt><tt class="py-op">,</tt> <tt class="py-name">keep_mask</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L67"></a><tt class="py-lineno">  67</tt>  <tt class="py-line">                                       <tt class="py-name">shrink</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno">  68</tt>  <tt class="py-line">        <tt class="py-name">subarr</tt> <tt class="py-op">=</tt> <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">view</tt><tt class="py-op">(</tt><tt class="py-name">subtype</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno">  69</tt>  <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno">  70</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-string">'folded'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno">  71</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">data_folded</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">data_folded</tt> <tt class="py-op">==</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno">  72</tt>  <tt class="py-line">                <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> </tt>
<a name="L73"></a><tt class="py-lineno">  73</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">data_folded</tt> <tt class="py-op">!=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno">  74</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Data does not have same folding status as '</tt> </tt>
<a name="L75"></a><tt class="py-lineno">  75</tt>  <tt class="py-line">                                 <tt class="py-string">'was called for in Spectrum constructor.'</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno">  76</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">data_folded</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno">  77</tt>  <tt class="py-line">            <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">data_folded</tt> </tt>
<a name="L78"></a><tt class="py-lineno">  78</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno">  79</tt>  <tt class="py-line">            <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L80"></a><tt class="py-lineno">  80</tt>  <tt class="py-line"> </tt>
<a name="L81"></a><tt class="py-lineno">  81</tt>  <tt class="py-line">        <tt class="py-comment"># Check that if we're declaring that the input data is folded, it</tt> </tt>
<a name="L82"></a><tt class="py-lineno">  82</tt>  <tt class="py-line">        <tt class="py-comment"># actually is, and the mask reflects this.</tt> </tt>
<a name="L83"></a><tt class="py-lineno">  83</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">data_folded</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno">  84</tt>  <tt class="py-line">            <tt class="py-name">total_samples</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.sample_sizes()=dadi.Spectrum_mod.Spectrum-class.html#sample_sizes"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-9', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno">  85</tt>  <tt class="py-line">            <tt class="py-name">total_per_entry</tt> <tt class="py-op">=</tt> <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum._total_per_entry()=dadi.Spectrum_mod.Spectrum-class.html#_total_per_entry"><a title="dadi.Spectrum_mod.Spectrum._total_per_entry" class="py-name" href="#" onclick="return doclink('link-10', '_total_per_entry', 'link-10');">_total_per_entry</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno">  86</tt>  <tt class="py-line">            <tt class="py-comment"># Which entries are nonsense in the folded fs.</tt> </tt>
<a name="L87"></a><tt class="py-lineno">  87</tt>  <tt class="py-line">            <tt class="py-name">where_folded_out</tt> <tt class="py-op">=</tt> <tt class="py-name">total_per_entry</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">total_samples</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno">  88</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">check_folding</tt>\ </tt>
<a name="L89"></a><tt class="py-lineno">  89</tt>  <tt class="py-line">               <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">all</tt><tt class="py-op">(</tt><tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">where_folded_out</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno">  90</tt>  <tt class="py-line">                <tt id="link-11" class="py-name"><a title="dadi.Hessian.logger
dadi.Inference.logger
dadi.Integration.logger
dadi.Numerics.logger
dadi.RunInParallel.logger
dadi.Spectrum_mod.logger" class="py-name" href="#" onclick="return doclink('link-11', 'logger', 'link-0');">logger</a></tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">'Creating Spectrum with data_folded = True, but '</tt> </tt>
<a name="L91"></a><tt class="py-lineno">  91</tt>  <tt class="py-line">                            <tt class="py-string">'data has non-zero values in entries which are '</tt> </tt>
<a name="L92"></a><tt class="py-lineno">  92</tt>  <tt class="py-line">                            <tt class="py-string">'nonsensical for a folded Spectrum.'</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno">  93</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">check_folding</tt>\ </tt>
<a name="L94"></a><tt class="py-lineno">  94</tt>  <tt class="py-line">               <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">all</tt><tt class="py-op">(</tt><tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">[</tt><tt class="py-name">where_folded_out</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno">  95</tt>  <tt class="py-line">                <tt id="link-12" class="py-name"><a title="dadi.Hessian.logger
dadi.Inference.logger
dadi.Integration.logger
dadi.Numerics.logger
dadi.RunInParallel.logger
dadi.Spectrum_mod.logger" class="py-name" href="#" onclick="return doclink('link-12', 'logger', 'link-0');">logger</a></tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">'Creating Spectrum with data_folded = True, but '</tt> </tt>
<a name="L96"></a><tt class="py-lineno">  96</tt>  <tt class="py-line">                            <tt class="py-string">'mask is not True for all entries which are '</tt> </tt>
<a name="L97"></a><tt class="py-lineno">  97</tt>  <tt class="py-line">                            <tt class="py-string">'nonsensical for a folded Spectrum.'</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno">  98</tt>  <tt class="py-line"> </tt>
<a name="L99"></a><tt class="py-lineno">  99</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-string">'pop_ids'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno"> 100</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">pop_ids</tt> <tt class="py-op">==</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno"> 101</tt>  <tt class="py-line">                <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L102"></a><tt class="py-lineno"> 102</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">pop_ids</tt> <tt class="py-op">!=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno"> 103</tt>  <tt class="py-line">                <tt id="link-13" class="py-name"><a title="dadi.Hessian.logger
dadi.Inference.logger
dadi.Integration.logger
dadi.Numerics.logger
dadi.RunInParallel.logger
dadi.Spectrum_mod.logger" class="py-name" href="#" onclick="return doclink('link-13', 'logger', 'link-0');">logger</a></tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">'Changing population labels in construction of new '</tt> </tt>
<a name="L104"></a><tt class="py-lineno"> 104</tt>  <tt class="py-line">                            <tt class="py-string">'Spectrum.'</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno"> 105</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno"> 106</tt>  <tt class="py-line">                    <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'pop_ids must be of length equal to '</tt> </tt>
<a name="L107"></a><tt class="py-lineno"> 107</tt>  <tt class="py-line">                                     <tt class="py-string">'dimensionality of Spectrum.'</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno"> 108</tt>  <tt class="py-line">                <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">pop_ids</tt> </tt>
<a name="L109"></a><tt class="py-lineno"> 109</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno"> 110</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno"> 111</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'pop_ids must be of length equal to '</tt> </tt>
<a name="L112"></a><tt class="py-lineno"> 112</tt>  <tt class="py-line">                                 <tt class="py-string">'dimensionality of Spectrum.'</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno"> 113</tt>  <tt class="py-line">            <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">pop_ids</tt> </tt>
<a name="L114"></a><tt class="py-lineno"> 114</tt>  <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno"> 115</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-14" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.mask_corners()=dadi.Spectrum_mod.Spectrum-class.html#mask_corners"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-14', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno"> 116</tt>  <tt class="py-line">            <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-15', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno"> 117</tt>  <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno"> 118</tt>  <tt class="py-line">        <tt class="py-name">subarr</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">extrap_x</tt> </tt>
<a name="L119"></a><tt class="py-lineno"> 119</tt>  <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno"> 120</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">subarr</tt> </tt>
</div><a name="L121"></a><tt class="py-lineno"> 121</tt>  <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno"> 122</tt>  <tt class="py-line">    <tt class="py-comment"># See http://www.scipy.org/Subclasses for information on the</tt> </tt>
<a name="L123"></a><tt class="py-lineno"> 123</tt>  <tt class="py-line">    <tt class="py-comment"># __array_finalize__ and __array_wrap__ methods. I had to do some debugging</tt> </tt>
<a name="L124"></a><tt class="py-lineno"> 124</tt>  <tt class="py-line">    <tt class="py-comment"># myself to discover that I also needed _update_from.</tt> </tt>
<a name="L125"></a><tt class="py-lineno"> 125</tt>  <tt class="py-line">    <tt class="py-comment"># Also, see http://docs.scipy.org/doc/numpy/reference/arrays.classes.html</tt> </tt>
<a name="L126"></a><tt class="py-lineno"> 126</tt>  <tt class="py-line">    <tt class="py-comment"># Also, see http://docs.scipy.org/doc/numpy/user/basics.subclassing.html</tt> </tt>
<a name="L127"></a><tt class="py-lineno"> 127</tt>  <tt class="py-line">    <tt class="py-comment">#</tt> </tt>
<a name="L128"></a><tt class="py-lineno"> 128</tt>  <tt class="py-line">    <tt class="py-comment"># We need these methods to ensure extra attributes get copied along when</tt> </tt>
<a name="L129"></a><tt class="py-lineno"> 129</tt>  <tt class="py-line">    <tt class="py-comment"># we do arithmetic on the FS.</tt> </tt>
<a name="Spectrum.__array_finalize__"></a><div id="Spectrum.__array_finalize__-def"><a name="L130"></a><tt class="py-lineno"> 130</tt> <a class="py-toggle" href="#" id="Spectrum.__array_finalize__-toggle" onclick="return toggle('Spectrum.__array_finalize__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#__array_finalize__">__array_finalize__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.__array_finalize__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.__array_finalize__-expanded"><a name="L131"></a><tt class="py-lineno"> 131</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">obj</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt>  </tt>
<a name="L132"></a><tt class="py-lineno"> 132</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L133"></a><tt class="py-lineno"> 133</tt>  <tt class="py-line">        <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_array</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.__array_finalize__()=dadi.Spectrum_mod.Spectrum-class.html#__array_finalize__"><a title="dadi.Spectrum_mod.Spectrum.__array_finalize__" class="py-name" href="#" onclick="return doclink('link-16', '__array_finalize__', 'link-16');">__array_finalize__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">obj</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno"> 134</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-string">'folded'</tt><tt class="py-op">,</tt> <tt class="py-string">'unspecified'</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno"> 135</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-string">'pop_ids'</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno"> 136</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-string">'extrap_x'</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div><a name="Spectrum.__array_wrap__"></a><div id="Spectrum.__array_wrap__-def"><a name="L137"></a><tt class="py-lineno"> 137</tt> <a class="py-toggle" href="#" id="Spectrum.__array_wrap__-toggle" onclick="return toggle('Spectrum.__array_wrap__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#__array_wrap__">__array_wrap__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">,</tt> <tt class="py-param">context</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.__array_wrap__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.__array_wrap__-expanded"><a name="L138"></a><tt class="py-lineno"> 138</tt>  <tt class="py-line">        <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">obj</tt><tt class="py-op">.</tt><tt class="py-name">view</tt><tt class="py-op">(</tt><tt class="py-name">type</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno"> 139</tt>  <tt class="py-line">        <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_array</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.__array_wrap__()=dadi.Spectrum_mod.Spectrum-class.html#__array_wrap__"><a title="dadi.Spectrum_mod.Spectrum.__array_wrap__" class="py-name" href="#" onclick="return doclink('link-17', '__array_wrap__', 'link-17');">__array_wrap__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">obj</tt><tt class="py-op">,</tt>  </tt>
<a name="L140"></a><tt class="py-lineno"> 140</tt>  <tt class="py-line">                                                      <tt class="py-name">context</tt><tt class="py-op">=</tt><tt class="py-name">context</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno"> 141</tt>  <tt class="py-line">        <tt class="py-name">result</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> </tt>
<a name="L142"></a><tt class="py-lineno"> 142</tt>  <tt class="py-line">        <tt class="py-name">result</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L143"></a><tt class="py-lineno"> 143</tt>  <tt class="py-line">        <tt class="py-name">result</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> </tt>
<a name="L144"></a><tt class="py-lineno"> 144</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
</div><a name="Spectrum._update_from"></a><div id="Spectrum._update_from-def"><a name="L145"></a><tt class="py-lineno"> 145</tt> <a class="py-toggle" href="#" id="Spectrum._update_from-toggle" onclick="return toggle('Spectrum._update_from');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_update_from">_update_from</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">obj</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._update_from-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._update_from-expanded"><a name="L146"></a><tt class="py-lineno"> 146</tt>  <tt class="py-line">        <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_array</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum._update_from()=dadi.Spectrum_mod.Spectrum-class.html#_update_from"><a title="dadi.Spectrum_mod.Spectrum._update_from" class="py-name" href="#" onclick="return doclink('link-18', '_update_from', 'link-18');">_update_from</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">obj</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno"> 147</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-string">'folded'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno"> 148</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">obj</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> </tt>
<a name="L149"></a><tt class="py-lineno"> 149</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-string">'pop_ids'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno"> 150</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">obj</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L151"></a><tt class="py-lineno"> 151</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">obj</tt><tt class="py-op">,</tt> <tt class="py-string">'extrap_x'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno"> 152</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">obj</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> </tt>
</div><a name="L153"></a><tt class="py-lineno"> 153</tt>  <tt class="py-line">    <tt class="py-comment"># masked_array has priority 15.</tt> </tt>
<a name="L154"></a><tt class="py-lineno"> 154</tt>  <tt class="py-line">    <tt id="link-19" class="py-name" targets="Variable dadi.Spectrum_mod.Spectrum.__array_priority__=dadi.Spectrum_mod.Spectrum-class.html#__array_priority__"><a title="dadi.Spectrum_mod.Spectrum.__array_priority__" class="py-name" href="#" onclick="return doclink('link-19', '__array_priority__', 'link-19');">__array_priority__</a></tt> <tt class="py-op">=</tt> <tt class="py-number">20</tt> </tt>
<a name="L155"></a><tt class="py-lineno"> 155</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.__repr__"></a><div id="Spectrum.__repr__-def"><a name="L156"></a><tt class="py-lineno"> 156</tt> <a class="py-toggle" href="#" id="Spectrum.__repr__-toggle" onclick="return toggle('Spectrum.__repr__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.__repr__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.__repr__-expanded"><a name="L157"></a><tt class="py-lineno"> 157</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-string">'Spectrum(%s, folded=%s, pop_ids=%s)'</tt>\ </tt>
<a name="L158"></a><tt class="py-lineno"> 158</tt>  <tt class="py-line">                <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L159"></a><tt class="py-lineno"> 159</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.mask_corners"></a><div id="Spectrum.mask_corners-def"><a name="L160"></a><tt class="py-lineno"> 160</tt> <a class="py-toggle" href="#" id="Spectrum.mask_corners-toggle" onclick="return toggle('Spectrum.mask_corners');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#mask_corners">mask_corners</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.mask_corners-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.mask_corners-expanded"><a name="L161"></a><tt class="py-lineno"> 161</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L162"></a><tt class="py-lineno"> 162</tt>  <tt class="py-line"><tt class="py-docstring">        Mask the 'seen in 0 samples' and 'seen in all samples' entries.</tt> </tt>
<a name="L163"></a><tt class="py-lineno"> 163</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L164"></a><tt class="py-lineno"> 164</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">.</tt><tt class="py-name">flat</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">.</tt><tt class="py-name">flat</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
</div><a name="L165"></a><tt class="py-lineno"> 165</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.unmask_all"></a><div id="Spectrum.unmask_all-def"><a name="L166"></a><tt class="py-lineno"> 166</tt> <a class="py-toggle" href="#" id="Spectrum.unmask_all-toggle" onclick="return toggle('Spectrum.unmask_all');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#unmask_all">unmask_all</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.unmask_all-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.unmask_all-expanded"><a name="L167"></a><tt class="py-lineno"> 167</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L168"></a><tt class="py-lineno"> 168</tt>  <tt class="py-line"><tt class="py-docstring">        Unmask all values.</tt> </tt>
<a name="L169"></a><tt class="py-lineno"> 169</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L170"></a><tt class="py-lineno"> 170</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.Npop()=dadi.Spectrum_mod.Spectrum-class.html#Npop"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-20', 'Npop', 'link-20');">Npop</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L171"></a><tt class="py-lineno"> 171</tt>  <tt class="py-line"> </tt>
<a name="Spectrum._get_sample_sizes"></a><div id="Spectrum._get_sample_sizes-def"><a name="L172"></a><tt class="py-lineno"> 172</tt> <a class="py-toggle" href="#" id="Spectrum._get_sample_sizes-toggle" onclick="return toggle('Spectrum._get_sample_sizes');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_get_sample_sizes">_get_sample_sizes</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._get_sample_sizes-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._get_sample_sizes-expanded"><a name="L173"></a><tt class="py-lineno"> 173</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L174"></a><tt class="py-lineno"> 174</tt>  <tt class="py-line">    <tt id="link-21" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-21', 'sample_sizes', 'link-9');">sample_sizes</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum._get_sample_sizes()=dadi.Spectrum_mod.Spectrum-class.html#_get_sample_sizes"><a title="dadi.Spectrum_mod.Spectrum._get_sample_sizes" class="py-name" href="#" onclick="return doclink('link-22', '_get_sample_sizes', 'link-22');">_get_sample_sizes</a></tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno"> 175</tt>  <tt class="py-line"> </tt>
<a name="Spectrum._get_Npop"></a><div id="Spectrum._get_Npop-def"><a name="L176"></a><tt class="py-lineno"> 176</tt> <a class="py-toggle" href="#" id="Spectrum._get_Npop-toggle" onclick="return toggle('Spectrum._get_Npop');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_get_Npop">_get_Npop</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._get_Npop-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._get_Npop-expanded"><a name="L177"></a><tt class="py-lineno"> 177</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt> </tt>
</div><a name="L178"></a><tt class="py-lineno"> 178</tt>  <tt class="py-line">    <tt id="link-23" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-23', 'Npop', 'link-20');">Npop</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-24" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum._get_Npop()=dadi.Spectrum_mod.Spectrum-class.html#_get_Npop"><a title="dadi.Spectrum_mod.Spectrum._get_Npop" class="py-name" href="#" onclick="return doclink('link-24', '_get_Npop', 'link-24');">_get_Npop</a></tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno"> 179</tt>  <tt class="py-line"> </tt>
<a name="Spectrum._ensure_dimension"></a><div id="Spectrum._ensure_dimension-def"><a name="L180"></a><tt class="py-lineno"> 180</tt> <a class="py-toggle" href="#" id="Spectrum._ensure_dimension-toggle" onclick="return toggle('Spectrum._ensure_dimension');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_ensure_dimension">_ensure_dimension</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">Npop</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._ensure_dimension-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._ensure_dimension-expanded"><a name="L181"></a><tt class="py-lineno"> 181</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L182"></a><tt class="py-lineno"> 182</tt>  <tt class="py-line"><tt class="py-docstring">        Ensure that fs has Npop dimensions.</tt> </tt>
<a name="L183"></a><tt class="py-lineno"> 183</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L184"></a><tt class="py-lineno"> 184</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-25', 'Npop', 'link-20');">Npop</a></tt> <tt class="py-op">==</tt> <tt id="link-26" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-26', 'Npop', 'link-20');">Npop</a></tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno"> 185</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Only compatible with %id spectra.'</tt> <tt class="py-op">%</tt> <tt id="link-27" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-27', 'Npop', 'link-20');">Npop</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L186"></a><tt class="py-lineno"> 186</tt>  <tt class="py-line"> </tt>
<a name="L187"></a><tt class="py-lineno"> 187</tt>  <tt class="py-line">    <tt class="py-comment"># Make from_file a static method, so we can use it without an instance.</tt> </tt>
<a name="L188"></a><tt class="py-lineno"> 188</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum.from_file"></a><div id="Spectrum.from_file-def"><a name="L189"></a><tt class="py-lineno"> 189</tt> <a class="py-toggle" href="#" id="Spectrum.from_file-toggle" onclick="return toggle('Spectrum.from_file');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#from_file">from_file</a><tt class="py-op">(</tt><tt class="py-param">fid</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-param">return_comments</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.from_file-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.from_file-expanded"><a name="L190"></a><tt class="py-lineno"> 190</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L191"></a><tt class="py-lineno"> 191</tt>  <tt class="py-line"><tt class="py-docstring">        Read frequency spectrum from file.</tt> </tt>
<a name="L192"></a><tt class="py-lineno"> 192</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L193"></a><tt class="py-lineno"> 193</tt>  <tt class="py-line"><tt class="py-docstring">        fid: string with file name to read from or an open file object.</tt> </tt>
<a name="L194"></a><tt class="py-lineno"> 194</tt>  <tt class="py-line"><tt class="py-docstring">        mask_corners: If True, mask the 'absent in all samples' and 'fixed in</tt> </tt>
<a name="L195"></a><tt class="py-lineno"> 195</tt>  <tt class="py-line"><tt class="py-docstring">                      all samples' entries.</tt> </tt>
<a name="L196"></a><tt class="py-lineno"> 196</tt>  <tt class="py-line"><tt class="py-docstring">        return_comments: If true, the return value is (fs, comments), where</tt> </tt>
<a name="L197"></a><tt class="py-lineno"> 197</tt>  <tt class="py-line"><tt class="py-docstring">                         comments is a list of strings containing the comments</tt> </tt>
<a name="L198"></a><tt class="py-lineno"> 198</tt>  <tt class="py-line"><tt class="py-docstring">                         from the file (without #'s).</tt> </tt>
<a name="L199"></a><tt class="py-lineno"> 199</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L200"></a><tt class="py-lineno"> 200</tt>  <tt class="py-line"><tt class="py-docstring">        See to_file method for details on the file format.</tt> </tt>
<a name="L201"></a><tt class="py-lineno"> 201</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L202"></a><tt class="py-lineno"> 202</tt>  <tt class="py-line">        <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L203"></a><tt class="py-lineno"> 203</tt>  <tt class="py-line">        <tt class="py-comment"># Try to read from fid. If we can't, assume it's something that we can</tt> </tt>
<a name="L204"></a><tt class="py-lineno"> 204</tt>  <tt class="py-line">        <tt class="py-comment"># use to open a file.</tt> </tt>
<a name="L205"></a><tt class="py-lineno"> 205</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'read'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno"> 206</tt>  <tt class="py-line">            <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L207"></a><tt class="py-lineno"> 207</tt>  <tt class="py-line">            <tt class="py-name">fid</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno"> 208</tt>  <tt class="py-line"> </tt>
<a name="L209"></a><tt class="py-lineno"> 209</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno"> 210</tt>  <tt class="py-line">        <tt class="py-comment"># Strip out the comments</tt> </tt>
<a name="L211"></a><tt class="py-lineno"> 211</tt>  <tt class="py-line">        <tt class="py-name">comments</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L212"></a><tt class="py-lineno"> 212</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'#'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno"> 213</tt>  <tt class="py-line">            <tt class="py-name">comments</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno"> 214</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno"> 215</tt>  <tt class="py-line"> </tt>
<a name="L216"></a><tt class="py-lineno"> 216</tt>  <tt class="py-line">        <tt class="py-comment"># Read the shape of the data</tt> </tt>
<a name="L217"></a><tt class="py-lineno"> 217</tt>  <tt class="py-line">        <tt class="py-name">shape_spl</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno"> 218</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-string">'folded'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">shape_spl</tt> <tt class="py-keyword">and</tt> <tt class="py-string">'unfolded'</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">shape_spl</tt><tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno"> 219</tt>  <tt class="py-line">            <tt class="py-comment"># This case handles the old file format</tt> </tt>
<a name="L220"></a><tt class="py-lineno"> 220</tt>  <tt class="py-line">            <tt class="py-name">shape</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">d</tt> <tt class="py-keyword">in</tt> <tt class="py-name">shape_spl</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno"> 221</tt>  <tt class="py-line">            <tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L222"></a><tt class="py-lineno"> 222</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L223"></a><tt class="py-lineno"> 223</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L224"></a><tt class="py-lineno"> 224</tt>  <tt class="py-line">            <tt class="py-comment"># This case handles the new file format</tt> </tt>
<a name="L225"></a><tt class="py-lineno"> 225</tt>  <tt class="py-line">            <tt class="py-name">shape</tt><tt class="py-op">,</tt><tt class="py-name">next_ii</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">shape_spl</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt> </tt>
<a name="L226"></a><tt class="py-lineno"> 226</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-name">shape_spl</tt><tt class="py-op">[</tt><tt class="py-name">next_ii</tt><tt class="py-op">]</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">'folded'</tt><tt class="py-op">,</tt> <tt class="py-string">'unfolded'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno"> 227</tt>  <tt class="py-line">                <tt class="py-name">shape</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">shape_spl</tt><tt class="py-op">[</tt><tt class="py-name">next_ii</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno"> 228</tt>  <tt class="py-line">                <tt class="py-name">next_ii</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L229"></a><tt class="py-lineno"> 229</tt>  <tt class="py-line">            <tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">shape_spl</tt><tt class="py-op">[</tt><tt class="py-name">next_ii</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'folded'</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno"> 230</tt>  <tt class="py-line">            <tt class="py-comment"># Are there population labels in the file?</tt> </tt>
<a name="L231"></a><tt class="py-lineno"> 231</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">shape_spl</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">next_ii</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno"> 232</tt>  <tt class="py-line">                <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">'"'</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L233"></a><tt class="py-lineno"> 233</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L234"></a><tt class="py-lineno"> 234</tt>  <tt class="py-line">                <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L235"></a><tt class="py-lineno"> 235</tt>  <tt class="py-line"> </tt>
<a name="L236"></a><tt class="py-lineno"> 236</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">fromstring</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L237"></a><tt class="py-lineno"> 237</tt>  <tt class="py-line">                                <tt class="py-name">count</tt><tt class="py-op">=</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">product</tt><tt class="py-op">(</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno"> 238</tt>  <tt class="py-line">        <tt class="py-comment"># fromfile returns a 1-d array. Reshape it to the proper form.</tt> </tt>
<a name="L239"></a><tt class="py-lineno"> 239</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno"> 240</tt>  <tt class="py-line"> </tt>
<a name="L241"></a><tt class="py-lineno"> 241</tt>  <tt class="py-line">        <tt class="py-name">maskline</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno"> 242</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">maskline</tt><tt class="py-op">:</tt> </tt>
<a name="L243"></a><tt class="py-lineno"> 243</tt>  <tt class="py-line">            <tt class="py-comment"># The old file format didn't have a line for the mask</tt> </tt>
<a name="L244"></a><tt class="py-lineno"> 244</tt>  <tt class="py-line">            <tt class="py-name">mask</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L245"></a><tt class="py-lineno"> 245</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno"> 246</tt>  <tt class="py-line">            <tt class="py-comment"># This case handles the new file format</tt> </tt>
<a name="L247"></a><tt class="py-lineno"> 247</tt>  <tt class="py-line">            <tt class="py-name">mask</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">fromstring</tt><tt class="py-op">(</tt><tt class="py-name">maskline</tt><tt class="py-op">,</tt>  </tt>
<a name="L248"></a><tt class="py-lineno"> 248</tt>  <tt class="py-line">                                    <tt class="py-name">count</tt><tt class="py-op">=</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">product</tt><tt class="py-op">(</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">=</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno"> 249</tt>  <tt class="py-line">            <tt class="py-name">mask</tt> <tt class="py-op">=</tt> <tt class="py-name">mask</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno"> 250</tt>  <tt class="py-line"> </tt>
<a name="L251"></a><tt class="py-lineno"> 251</tt>  <tt class="py-line">        <tt class="py-comment"># If we opened a new file, clean it up.</tt> </tt>
<a name="L252"></a><tt class="py-lineno"> 252</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">newfile</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno"> 253</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L254"></a><tt class="py-lineno"> 254</tt>  <tt class="py-line"> </tt>
<a name="L255"></a><tt class="py-lineno"> 255</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name" targets="Variable dadi.Demographics1D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Variable dadi.Demographics2D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Class dadi.Spectrum_mod.Spectrum=dadi.Spectrum_mod.Spectrum-class.html"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-28', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">mask</tt><tt class="py-op">,</tt> <tt id="link-29" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-29', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt> <tt class="py-name">data_folded</tt><tt class="py-op">=</tt><tt class="py-name">folded</tt><tt class="py-op">,</tt> </tt>
<a name="L256"></a><tt class="py-lineno"> 256</tt>  <tt class="py-line">                      <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno"> 257</tt>  <tt class="py-line"> </tt>
<a name="L258"></a><tt class="py-lineno"> 258</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">return_comments</tt><tt class="py-op">:</tt> </tt>
<a name="L259"></a><tt class="py-lineno"> 259</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
<a name="L260"></a><tt class="py-lineno"> 260</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno"> 261</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt><tt class="py-op">,</tt><tt class="py-name">comments</tt> </tt>
</div><a name="L262"></a><tt class="py-lineno"> 262</tt>  <tt class="py-line"> </tt>
<a name="L263"></a><tt class="py-lineno"> 263</tt>  <tt class="py-line">    <tt class="py-name">fromfile</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum.from_file()=dadi.Spectrum_mod.Spectrum-class.html#from_file"><a title="dadi.Spectrum_mod.Spectrum.from_file" class="py-name" href="#" onclick="return doclink('link-30', 'from_file', 'link-30');">from_file</a></tt> </tt>
<a name="L264"></a><tt class="py-lineno"> 264</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.to_file"></a><div id="Spectrum.to_file-def"><a name="L265"></a><tt class="py-lineno"> 265</tt> <a class="py-toggle" href="#" id="Spectrum.to_file-toggle" onclick="return toggle('Spectrum.to_file');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#to_file">to_file</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fid</tt><tt class="py-op">,</tt> <tt class="py-param">precision</tt><tt class="py-op">=</tt><tt class="py-number">16</tt><tt class="py-op">,</tt> <tt class="py-param">comment_lines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L266"></a><tt class="py-lineno"> 266</tt>  <tt class="py-line">                <tt class="py-param">foldmaskinfo</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.to_file-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.to_file-expanded"><a name="L267"></a><tt class="py-lineno"> 267</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L268"></a><tt class="py-lineno"> 268</tt>  <tt class="py-line"><tt class="py-docstring">        Write frequency spectrum to file.</tt> </tt>
<a name="L269"></a><tt class="py-lineno"> 269</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L270"></a><tt class="py-lineno"> 270</tt>  <tt class="py-line"><tt class="py-docstring">        fid: string with file name to write to or an open file object.</tt> </tt>
<a name="L271"></a><tt class="py-lineno"> 271</tt>  <tt class="py-line"><tt class="py-docstring">        precision: precision with which to write out entries of the SFS. (They </tt> </tt>
<a name="L272"></a><tt class="py-lineno"> 272</tt>  <tt class="py-line"><tt class="py-docstring">                   are formated via %.&lt;p&gt;g, where &lt;p&gt; is the precision.)</tt> </tt>
<a name="L273"></a><tt class="py-lineno"> 273</tt>  <tt class="py-line"><tt class="py-docstring">        comment lines: list of strings to be used as comment lines in the header</tt> </tt>
<a name="L274"></a><tt class="py-lineno"> 274</tt>  <tt class="py-line"><tt class="py-docstring">                       of the output file.</tt> </tt>
<a name="L275"></a><tt class="py-lineno"> 275</tt>  <tt class="py-line"><tt class="py-docstring">        foldmaskinfo: If False, folding and mask and population label</tt> </tt>
<a name="L276"></a><tt class="py-lineno"> 276</tt>  <tt class="py-line"><tt class="py-docstring">                      information will not be saved. This conforms to the file</tt> </tt>
<a name="L277"></a><tt class="py-lineno"> 277</tt>  <tt class="py-line"><tt class="py-docstring">                      format for dadi versions prior to 1.3.0.</tt> </tt>
<a name="L278"></a><tt class="py-lineno"> 278</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L279"></a><tt class="py-lineno"> 279</tt>  <tt class="py-line"><tt class="py-docstring">        The file format is:</tt> </tt>
<a name="L280"></a><tt class="py-lineno"> 280</tt>  <tt class="py-line"><tt class="py-docstring">            # Any number of comment lines beginning with a '#'</tt> </tt>
<a name="L281"></a><tt class="py-lineno"> 281</tt>  <tt class="py-line"><tt class="py-docstring">            A single line containing N integers giving the dimensions of the fs</tt> </tt>
<a name="L282"></a><tt class="py-lineno"> 282</tt>  <tt class="py-line"><tt class="py-docstring">              array. So this line would be '5 5 3' for an SFS that was 5x5x3.</tt> </tt>
<a name="L283"></a><tt class="py-lineno"> 283</tt>  <tt class="py-line"><tt class="py-docstring">              (That would be 4x4x2 *samples*.)</tt> </tt>
<a name="L284"></a><tt class="py-lineno"> 284</tt>  <tt class="py-line"><tt class="py-docstring">            On the *same line*, the string 'folded' or 'unfolded' denoting the</tt> </tt>
<a name="L285"></a><tt class="py-lineno"> 285</tt>  <tt class="py-line"><tt class="py-docstring">              folding status of the array</tt> </tt>
<a name="L286"></a><tt class="py-lineno"> 286</tt>  <tt class="py-line"><tt class="py-docstring">            On the *same line*, optional strings each containing the population</tt> </tt>
<a name="L287"></a><tt class="py-lineno"> 287</tt>  <tt class="py-line"><tt class="py-docstring">              labels in quotes separated by spaces, e.g. "pop 1" "pop 2"</tt> </tt>
<a name="L288"></a><tt class="py-lineno"> 288</tt>  <tt class="py-line"><tt class="py-docstring">            A single line giving the array elements. The order of elements is </tt> </tt>
<a name="L289"></a><tt class="py-lineno"> 289</tt>  <tt class="py-line"><tt class="py-docstring">              e.g.: fs[0,0,0] fs[0,0,1] fs[0,0,2] ... fs[0,1,0] fs[0,1,1] ...</tt> </tt>
<a name="L290"></a><tt class="py-lineno"> 290</tt>  <tt class="py-line"><tt class="py-docstring">            A single line giving the elements of the mask in the same order as</tt> </tt>
<a name="L291"></a><tt class="py-lineno"> 291</tt>  <tt class="py-line"><tt class="py-docstring">              the data line. '1' indicates masked, '0' indicates unmasked.</tt> </tt>
<a name="L292"></a><tt class="py-lineno"> 292</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L293"></a><tt class="py-lineno"> 293</tt>  <tt class="py-line">        <tt class="py-comment"># Open the file object.</tt> </tt>
<a name="L294"></a><tt class="py-lineno"> 294</tt>  <tt class="py-line">        <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L295"></a><tt class="py-lineno"> 295</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'write'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno"> 296</tt>  <tt class="py-line">            <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L297"></a><tt class="py-lineno"> 297</tt>  <tt class="py-line">            <tt class="py-name">fid</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L298"></a><tt class="py-lineno"> 298</tt>  <tt class="py-line"> </tt>
<a name="L299"></a><tt class="py-lineno"> 299</tt>  <tt class="py-line">        <tt class="py-comment"># Write comments</tt> </tt>
<a name="L300"></a><tt class="py-lineno"> 300</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">comment_lines</tt><tt class="py-op">:</tt> </tt>
<a name="L301"></a><tt class="py-lineno"> 301</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'# '</tt><tt class="py-op">)</tt> </tt>
<a name="L302"></a><tt class="py-lineno"> 302</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno"> 303</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">linesep</tt><tt class="py-op">)</tt> </tt>
<a name="L304"></a><tt class="py-lineno"> 304</tt>  <tt class="py-line"> </tt>
<a name="L305"></a><tt class="py-lineno"> 305</tt>  <tt class="py-line">        <tt class="py-comment"># Write out the shape of the fs</tt> </tt>
<a name="L306"></a><tt class="py-lineno"> 306</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">elem</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno"> 307</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'%i '</tt> <tt class="py-op">%</tt> <tt class="py-name">elem</tt><tt class="py-op">)</tt> </tt>
<a name="L308"></a><tt class="py-lineno"> 308</tt>  <tt class="py-line"> </tt>
<a name="L309"></a><tt class="py-lineno"> 309</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">foldmaskinfo</tt><tt class="py-op">:</tt> </tt>
<a name="L310"></a><tt class="py-lineno"> 310</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L311"></a><tt class="py-lineno"> 311</tt>  <tt class="py-line">                <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'unfolded'</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno"> 312</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L313"></a><tt class="py-lineno"> 313</tt>  <tt class="py-line">                <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'folded'</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno"> 314</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L315"></a><tt class="py-lineno"> 315</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">label</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno"> 316</tt>  <tt class="py-line">                    <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">' "%s"'</tt> <tt class="py-op">%</tt> <tt class="py-name">label</tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno"> 317</tt>  <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno"> 318</tt>  <tt class="py-line">        <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">linesep</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno"> 319</tt>  <tt class="py-line"> </tt>
<a name="L320"></a><tt class="py-lineno"> 320</tt>  <tt class="py-line">        <tt class="py-comment"># Write the data to the file</tt> </tt>
<a name="L321"></a><tt class="py-lineno"> 321</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">tofile</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">,</tt> <tt class="py-string">'%%.%ig'</tt> <tt class="py-op">%</tt> <tt class="py-name">precision</tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno"> 322</tt>  <tt class="py-line">        <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">linesep</tt><tt class="py-op">)</tt> </tt>
<a name="L323"></a><tt class="py-lineno"> 323</tt>  <tt class="py-line"> </tt>
<a name="L324"></a><tt class="py-lineno"> 324</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">foldmaskinfo</tt><tt class="py-op">:</tt> </tt>
<a name="L325"></a><tt class="py-lineno"> 325</tt>  <tt class="py-line">            <tt class="py-comment"># Write the mask to the file</tt> </tt>
<a name="L326"></a><tt class="py-lineno"> 326</tt>  <tt class="py-line">            <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">tofile</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L327"></a><tt class="py-lineno"> 327</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">linesep</tt><tt class="py-op">)</tt> </tt>
<a name="L328"></a><tt class="py-lineno"> 328</tt>  <tt class="py-line"> </tt>
<a name="L329"></a><tt class="py-lineno"> 329</tt>  <tt class="py-line">        <tt class="py-comment"># Close file</tt> </tt>
<a name="L330"></a><tt class="py-lineno"> 330</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">newfile</tt><tt class="py-op">:</tt> </tt>
<a name="L331"></a><tt class="py-lineno"> 331</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L332"></a><tt class="py-lineno"> 332</tt>  <tt class="py-line"> </tt>
<a name="L333"></a><tt class="py-lineno"> 333</tt>  <tt class="py-line">    <tt class="py-name">tofile</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.to_file()=dadi.Spectrum_mod.Spectrum-class.html#to_file"><a title="dadi.Spectrum_mod.Spectrum.to_file" class="py-name" href="#" onclick="return doclink('link-31', 'to_file', 'link-31');">to_file</a></tt> </tt>
<a name="L334"></a><tt class="py-lineno"> 334</tt>  <tt class="py-line"> </tt>
<a name="L335"></a><tt class="py-lineno"> 335</tt>  <tt class="py-line">    <tt class="py-comment">## Overide the (perhaps confusing) original numpy tofile method.</tt> </tt>
<a name="L336"></a><tt class="py-lineno"> 336</tt>  <tt class="py-line">    <tt class="py-comment">#def tofile(self, *args,**kwargs):</tt> </tt>
<a name="L337"></a><tt class="py-lineno"> 337</tt>  <tt class="py-line">    <tt class="py-comment">#    self.to_file(*args, **kwargs)</tt> </tt>
<a name="L338"></a><tt class="py-lineno"> 338</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.project"></a><div id="Spectrum.project-def"><a name="L339"></a><tt class="py-lineno"> 339</tt> <a class="py-toggle" href="#" id="Spectrum.project-toggle" onclick="return toggle('Spectrum.project');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#project">project</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.project-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.project-expanded"><a name="L340"></a><tt class="py-lineno"> 340</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L341"></a><tt class="py-lineno"> 341</tt>  <tt class="py-line"><tt class="py-docstring">        Project to smaller sample size.</tt> </tt>
<a name="L342"></a><tt class="py-lineno"> 342</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L343"></a><tt class="py-lineno"> 343</tt>  <tt class="py-line"><tt class="py-docstring">        ns: Sample sizes for new spectrum.</tt> </tt>
<a name="L344"></a><tt class="py-lineno"> 344</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L345"></a><tt class="py-lineno"> 345</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-32', 'Npop', 'link-20');">Npop</a></tt><tt class="py-op">:</tt> </tt>
<a name="L346"></a><tt class="py-lineno"> 346</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Requested sample sizes not of same dimension '</tt> </tt>
<a name="L347"></a><tt class="py-lineno"> 347</tt>  <tt class="py-line">                             <tt class="py-string">'as spectrum. Perhaps you need to marginalize '</tt> </tt>
<a name="L348"></a><tt class="py-lineno"> 348</tt>  <tt class="py-line">                             <tt class="py-string">'over some populations first?'</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno"> 349</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-33', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L350"></a><tt class="py-lineno"> 350</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Cannot project to a sample size greater than '</tt> </tt>
<a name="L351"></a><tt class="py-lineno"> 351</tt>  <tt class="py-line">                             <tt class="py-string">'original. Original size is %s and requested size '</tt> </tt>
<a name="L352"></a><tt class="py-lineno"> 352</tt>  <tt class="py-line">                             <tt class="py-string">'is %s.'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-34', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L353"></a><tt class="py-lineno"> 353</tt>  <tt class="py-line"> </tt>
<a name="L354"></a><tt class="py-lineno"> 354</tt>  <tt class="py-line">        <tt class="py-name">original_folded</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> </tt>
<a name="L355"></a><tt class="py-lineno"> 355</tt>  <tt class="py-line">        <tt class="py-comment"># If we started with an folded Spectrum, we need to unfold before</tt> </tt>
<a name="L356"></a><tt class="py-lineno"> 356</tt>  <tt class="py-line">        <tt class="py-comment"># projecting.</tt> </tt>
<a name="L357"></a><tt class="py-lineno"> 357</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">original_folded</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno"> 358</tt>  <tt class="py-line">            <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.unfold()=dadi.Spectrum_mod.Spectrum-class.html#unfold"><a title="dadi.Spectrum_mod.Spectrum.unfold" class="py-name" href="#" onclick="return doclink('link-35', 'unfold', 'link-35');">unfold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno"> 359</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno"> 360</tt>  <tt class="py-line">            <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">copy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L361"></a><tt class="py-lineno"> 361</tt>  <tt class="py-line"> </tt>
<a name="L362"></a><tt class="py-lineno"> 362</tt>  <tt class="py-line">        <tt class="py-comment"># Iterate over each axis, applying the projection.</tt> </tt>
<a name="L363"></a><tt class="py-lineno"> 363</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">axis</tt><tt class="py-op">,</tt><tt class="py-name">proj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L364"></a><tt class="py-lineno"> 364</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">proj</tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-36', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L365"></a><tt class="py-lineno"> 365</tt>  <tt class="py-line">                <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum._project_one_axis()=dadi.Spectrum_mod.Spectrum-class.html#_project_one_axis"><a title="dadi.Spectrum_mod.Spectrum._project_one_axis" class="py-name" href="#" onclick="return doclink('link-37', '_project_one_axis', 'link-37');">_project_one_axis</a></tt><tt class="py-op">(</tt><tt class="py-name">proj</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno"> 366</tt>  <tt class="py-line"> </tt>
<a name="L367"></a><tt class="py-lineno"> 367</tt>  <tt class="py-line">        <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> </tt>
<a name="L368"></a><tt class="py-lineno"> 368</tt>  <tt class="py-line">        <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> </tt>
<a name="L369"></a><tt class="py-lineno"> 369</tt>  <tt class="py-line"> </tt>
<a name="L370"></a><tt class="py-lineno"> 370</tt>  <tt class="py-line">        <tt class="py-comment"># Return folded or unfolded as original.</tt> </tt>
<a name="L371"></a><tt class="py-lineno"> 371</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">original_folded</tt><tt class="py-op">:</tt> </tt>
<a name="L372"></a><tt class="py-lineno"> 372</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.fold()=dadi.Spectrum_mod.Spectrum-class.html#fold"><a title="dadi.Spectrum_mod.Spectrum.fold" class="py-name" href="#" onclick="return doclink('link-38', 'fold', 'link-38');">fold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno"> 373</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L374"></a><tt class="py-lineno"> 374</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L375"></a><tt class="py-lineno"> 375</tt>  <tt class="py-line"> </tt>
<a name="Spectrum._project_one_axis"></a><div id="Spectrum._project_one_axis-def"><a name="L376"></a><tt class="py-lineno"> 376</tt> <a class="py-toggle" href="#" id="Spectrum._project_one_axis-toggle" onclick="return toggle('Spectrum._project_one_axis');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_project_one_axis">_project_one_axis</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">,</tt> <tt class="py-param">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._project_one_axis-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._project_one_axis-expanded"><a name="L377"></a><tt class="py-lineno"> 377</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L378"></a><tt class="py-lineno"> 378</tt>  <tt class="py-line"><tt class="py-docstring">        Project along a single axis.</tt> </tt>
<a name="L379"></a><tt class="py-lineno"> 379</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L380"></a><tt class="py-lineno"> 380</tt>  <tt class="py-line">        <tt class="py-comment"># This gets a little tricky with fancy indexing to make it work</tt> </tt>
<a name="L381"></a><tt class="py-lineno"> 381</tt>  <tt class="py-line">        <tt class="py-comment"># for fs with arbitrary number of dimensions.</tt> </tt>
<a name="L382"></a><tt class="py-lineno"> 382</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-39', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno"> 383</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Cannot project to a sample size greater than '</tt> </tt>
<a name="L384"></a><tt class="py-lineno"> 384</tt>  <tt class="py-line">                             <tt class="py-string">'original. Called sizes were from %s to %s.'</tt>  </tt>
<a name="L385"></a><tt class="py-lineno"> 385</tt>  <tt class="py-line">                             <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-40', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L386"></a><tt class="py-lineno"> 386</tt>  <tt class="py-line"> </tt>
<a name="L387"></a><tt class="py-lineno"> 387</tt>  <tt class="py-line">        <tt class="py-name">newshape</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno"> 388</tt>  <tt class="py-line">        <tt class="py-name">newshape</tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L389"></a><tt class="py-lineno"> 389</tt>  <tt class="py-line">        <tt class="py-comment"># Create a new empty fs that we'll fill in below.</tt> </tt>
<a name="L390"></a><tt class="py-lineno"> 390</tt>  <tt class="py-line">        <tt class="py-name">pfs</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-41', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">newshape</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-42', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L391"></a><tt class="py-lineno"> 391</tt>  <tt class="py-line"> </tt>
<a name="L392"></a><tt class="py-lineno"> 392</tt>  <tt class="py-line">        <tt class="py-comment"># Set up for our fancy indexes. These slices are currently like</tt> </tt>
<a name="L393"></a><tt class="py-lineno"> 393</tt>  <tt class="py-line">        <tt class="py-comment"># [:,:,...]</tt> </tt>
<a name="L394"></a><tt class="py-lineno"> 394</tt>  <tt class="py-line">        <tt class="py-name">from_slice</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-43', 'Npop', 'link-20');">Npop</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L395"></a><tt class="py-lineno"> 395</tt>  <tt class="py-line">        <tt class="py-name">to_slice</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-44', 'Npop', 'link-20');">Npop</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L396"></a><tt class="py-lineno"> 396</tt>  <tt class="py-line">        <tt class="py-name">proj_slice</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">nuax</tt> <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-45', 'Npop', 'link-20');">Npop</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L397"></a><tt class="py-lineno"> 397</tt>  <tt class="py-line"> </tt>
<a name="L398"></a><tt class="py-lineno"> 398</tt>  <tt class="py-line">        <tt class="py-name">proj_from</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-46', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt> </tt>
<a name="L399"></a><tt class="py-lineno"> 399</tt>  <tt class="py-line">        <tt class="py-comment"># For each possible number of hits.</tt> </tt>
<a name="L400"></a><tt class="py-lineno"> 400</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">hits</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">proj_from</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno"> 401</tt>  <tt class="py-line">            <tt class="py-comment"># Adjust the slice in the array we're projecting from.</tt> </tt>
<a name="L402"></a><tt class="py-lineno"> 402</tt>  <tt class="py-line">            <tt class="py-name">from_slice</tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">,</tt> <tt class="py-name">hits</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L403"></a><tt class="py-lineno"> 403</tt>  <tt class="py-line">            <tt class="py-comment"># These are the least and most possible hits we could have in the</tt> </tt>
<a name="L404"></a><tt class="py-lineno"> 404</tt>  <tt class="py-line">            <tt class="py-comment">#  projected fs.</tt> </tt>
<a name="L405"></a><tt class="py-lineno"> 405</tt>  <tt class="py-line">            <tt class="py-name">least</tt><tt class="py-op">,</tt> <tt class="py-name">most</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">n</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">proj_from</tt> <tt class="py-op">-</tt> <tt class="py-name">hits</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">hits</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L406"></a><tt class="py-lineno"> 406</tt>  <tt class="py-line">            <tt class="py-name">to_slice</tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">least</tt><tt class="py-op">,</tt> <tt class="py-name">most</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L407"></a><tt class="py-lineno"> 407</tt>  <tt class="py-line">            <tt class="py-comment"># The projection weights.</tt> </tt>
<a name="L408"></a><tt class="py-lineno"> 408</tt>  <tt class="py-line">            <tt class="py-name">proj</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="dadi.Numerics._cached_projection" class="py-name" href="#" onclick="return doclink('link-47', '_cached_projection', 'link-7');">_cached_projection</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-name">proj_from</tt><tt class="py-op">,</tt> <tt class="py-name">hits</tt><tt class="py-op">)</tt> </tt>
<a name="L409"></a><tt class="py-lineno"> 409</tt>  <tt class="py-line">            <tt class="py-name">proj_slice</tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">least</tt><tt class="py-op">,</tt> <tt class="py-name">most</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno"> 410</tt>  <tt class="py-line">            <tt class="py-comment"># Do the multiplications</tt> </tt>
<a name="L411"></a><tt class="py-lineno"> 411</tt>  <tt class="py-line">            <tt class="py-name">pfs</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">to_slice</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">from_slice</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">proj</tt><tt class="py-op">[</tt><tt class="py-name">proj_slice</tt><tt class="py-op">]</tt> </tt>
<a name="L412"></a><tt class="py-lineno"> 412</tt>  <tt class="py-line">            <tt class="py-name">pfs</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">[</tt><tt class="py-name">to_slice</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_or</tt><tt class="py-op">(</tt><tt class="py-name">pfs</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">[</tt><tt class="py-name">to_slice</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L413"></a><tt class="py-lineno"> 413</tt>  <tt class="py-line">                                                  <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">[</tt><tt class="py-name">from_slice</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L414"></a><tt class="py-lineno"> 414</tt>  <tt class="py-line">     </tt>
<a name="L415"></a><tt class="py-lineno"> 415</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">pfs</tt> </tt>
</div><a name="L416"></a><tt class="py-lineno"> 416</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.marginalize"></a><div id="Spectrum.marginalize-def"><a name="L417"></a><tt class="py-lineno"> 417</tt> <a class="py-toggle" href="#" id="Spectrum.marginalize-toggle" onclick="return toggle('Spectrum.marginalize');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#marginalize">marginalize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">over</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.marginalize-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.marginalize-expanded"><a name="L418"></a><tt class="py-lineno"> 418</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L419"></a><tt class="py-lineno"> 419</tt>  <tt class="py-line"><tt class="py-docstring">        Reduced dimensionality spectrum summing over some populations.</tt> </tt>
<a name="L420"></a><tt class="py-lineno"> 420</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L421"></a><tt class="py-lineno"> 421</tt>  <tt class="py-line"><tt class="py-docstring">        over: sequence of axes to sum over. For example (0,2) will sum over</tt> </tt>
<a name="L422"></a><tt class="py-lineno"> 422</tt>  <tt class="py-line"><tt class="py-docstring">              populations 0 and 2.</tt> </tt>
<a name="L423"></a><tt class="py-lineno"> 423</tt>  <tt class="py-line"><tt class="py-docstring">        mask_corners: If True, the typical corners of the resulting fs will be</tt> </tt>
<a name="L424"></a><tt class="py-lineno"> 424</tt>  <tt class="py-line"><tt class="py-docstring">                      masked</tt> </tt>
<a name="L425"></a><tt class="py-lineno"> 425</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L426"></a><tt class="py-lineno"> 426</tt>  <tt class="py-line">        <tt class="py-name">original_folded</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> </tt>
<a name="L427"></a><tt class="py-lineno"> 427</tt>  <tt class="py-line">        <tt class="py-comment"># If we started with an folded Spectrum, we need to unfold before</tt> </tt>
<a name="L428"></a><tt class="py-lineno"> 428</tt>  <tt class="py-line">        <tt class="py-comment"># marginalizing.</tt> </tt>
<a name="L429"></a><tt class="py-lineno"> 429</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">original_folded</tt><tt class="py-op">:</tt> </tt>
<a name="L430"></a><tt class="py-lineno"> 430</tt>  <tt class="py-line">            <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.unfold" class="py-name" href="#" onclick="return doclink('link-48', 'unfold', 'link-35');">unfold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno"> 431</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L432"></a><tt class="py-lineno"> 432</tt>  <tt class="py-line">            <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">copy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L433"></a><tt class="py-lineno"> 433</tt>  <tt class="py-line"> </tt>
<a name="L434"></a><tt class="py-lineno"> 434</tt>  <tt class="py-line">        <tt class="py-name">orig_mask</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">.</tt><tt class="py-name">copy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L435"></a><tt class="py-lineno"> 435</tt>  <tt class="py-line">        <tt class="py-name">orig_mask</tt><tt class="py-op">.</tt><tt class="py-name">flat</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">orig_mask</tt><tt class="py-op">.</tt><tt class="py-name">flat</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L436"></a><tt class="py-lineno"> 436</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-name">orig_mask</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L437"></a><tt class="py-lineno"> 437</tt>  <tt class="py-line">            <tt id="link-49" class="py-name"><a title="dadi.Hessian.logger
dadi.Inference.logger
dadi.Integration.logger
dadi.Numerics.logger
dadi.RunInParallel.logger
dadi.Spectrum_mod.logger" class="py-name" href="#" onclick="return doclink('link-49', 'logger', 'link-0');">logger</a></tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">'Marginalizing a Spectrum with internal masked values. '</tt> </tt>
<a name="L438"></a><tt class="py-lineno"> 438</tt>  <tt class="py-line">                        <tt class="py-string">'This may not be a well-defined operation.'</tt><tt class="py-op">)</tt> </tt>
<a name="L439"></a><tt class="py-lineno"> 439</tt>  <tt class="py-line"> </tt>
<a name="L440"></a><tt class="py-lineno"> 440</tt>  <tt class="py-line">        <tt class="py-comment"># Do the marginalization</tt> </tt>
<a name="L441"></a><tt class="py-lineno"> 441</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">axis</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sorted</tt><tt class="py-op">(</tt><tt class="py-name">over</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno"> 442</tt>  <tt class="py-line">            <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-name">axis</tt><tt class="py-op">)</tt> </tt>
<a name="L443"></a><tt class="py-lineno"> 443</tt>  <tt class="py-line">        <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L444"></a><tt class="py-lineno"> 444</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L445"></a><tt class="py-lineno"> 445</tt>  <tt class="py-line">            <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L446"></a><tt class="py-lineno"> 446</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">axis</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sorted</tt><tt class="py-op">(</tt><tt class="py-name">over</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L447"></a><tt class="py-lineno"> 447</tt>  <tt class="py-line">                <tt class="py-keyword">del</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">[</tt><tt class="py-name">axis</tt><tt class="py-op">]</tt> </tt>
<a name="L448"></a><tt class="py-lineno"> 448</tt>  <tt class="py-line">        <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L449"></a><tt class="py-lineno"> 449</tt>  <tt class="py-line">        <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">pop_ids</tt> </tt>
<a name="L450"></a><tt class="py-lineno"> 450</tt>  <tt class="py-line">        <tt class="py-name">output</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> </tt>
<a name="L451"></a><tt class="py-lineno"> 451</tt>  <tt class="py-line"> </tt>
<a name="L452"></a><tt class="py-lineno"> 452</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-50" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-50', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">:</tt> </tt>
<a name="L453"></a><tt class="py-lineno"> 453</tt>  <tt class="py-line">            <tt class="py-name">output</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-51', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L454"></a><tt class="py-lineno"> 454</tt>  <tt class="py-line"> </tt>
<a name="L455"></a><tt class="py-lineno"> 455</tt>  <tt class="py-line">        <tt class="py-comment"># Return folded or unfolded as original.</tt> </tt>
<a name="L456"></a><tt class="py-lineno"> 456</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">original_folded</tt><tt class="py-op">:</tt> </tt>
<a name="L457"></a><tt class="py-lineno"> 457</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">output</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.fold" class="py-name" href="#" onclick="return doclink('link-52', 'fold', 'link-38');">fold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L458"></a><tt class="py-lineno"> 458</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L459"></a><tt class="py-lineno"> 459</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div><a name="L460"></a><tt class="py-lineno"> 460</tt>  <tt class="py-line"> </tt>
<a name="Spectrum._counts_per_entry"></a><div id="Spectrum._counts_per_entry-def"><a name="L461"></a><tt class="py-lineno"> 461</tt> <a class="py-toggle" href="#" id="Spectrum._counts_per_entry-toggle" onclick="return toggle('Spectrum._counts_per_entry');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_counts_per_entry">_counts_per_entry</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._counts_per_entry-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._counts_per_entry-expanded"><a name="L462"></a><tt class="py-lineno"> 462</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L463"></a><tt class="py-lineno"> 463</tt>  <tt class="py-line"><tt class="py-docstring">        Counts per population for each entry in the fs.</tt> </tt>
<a name="L464"></a><tt class="py-lineno"> 464</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L465"></a><tt class="py-lineno"> 465</tt>  <tt class="py-line">        <tt class="py-name">ind</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">indices</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L466"></a><tt class="py-lineno"> 466</tt>  <tt class="py-line">        <tt class="py-comment"># Transpose the first access to the last, so ind[ii,jj,kk] = [ii,jj,kk]</tt> </tt>
<a name="L467"></a><tt class="py-lineno"> 467</tt>  <tt class="py-line">        <tt class="py-name">ind</tt> <tt class="py-op">=</tt> <tt class="py-name">ind</tt><tt class="py-op">.</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-53', 'Npop', 'link-20');">Npop</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L468"></a><tt class="py-lineno"> 468</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">ind</tt> </tt>
</div><a name="L469"></a><tt class="py-lineno"> 469</tt>  <tt class="py-line"> </tt>
<a name="Spectrum._total_per_entry"></a><div id="Spectrum._total_per_entry-def"><a name="L470"></a><tt class="py-lineno"> 470</tt> <a class="py-toggle" href="#" id="Spectrum._total_per_entry-toggle" onclick="return toggle('Spectrum._total_per_entry');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_total_per_entry">_total_per_entry</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._total_per_entry-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._total_per_entry-expanded"><a name="L471"></a><tt class="py-lineno"> 471</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L472"></a><tt class="py-lineno"> 472</tt>  <tt class="py-line"><tt class="py-docstring">        Total derived alleles for each entry in the fs.</tt> </tt>
<a name="L473"></a><tt class="py-lineno"> 473</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L474"></a><tt class="py-lineno"> 474</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum._counts_per_entry()=dadi.Spectrum_mod.Spectrum-class.html#_counts_per_entry"><a title="dadi.Spectrum_mod.Spectrum._counts_per_entry" class="py-name" href="#" onclick="return doclink('link-54', '_counts_per_entry', 'link-54');">_counts_per_entry</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L475"></a><tt class="py-lineno"> 475</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.fold"></a><div id="Spectrum.fold-def"><a name="L476"></a><tt class="py-lineno"> 476</tt> <a class="py-toggle" href="#" id="Spectrum.fold-toggle" onclick="return toggle('Spectrum.fold');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#fold">fold</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.fold-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.fold-expanded"><a name="L477"></a><tt class="py-lineno"> 477</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L478"></a><tt class="py-lineno"> 478</tt>  <tt class="py-line"><tt class="py-docstring">        Folded frequency spectrum</tt> </tt>
<a name="L479"></a><tt class="py-lineno"> 479</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L480"></a><tt class="py-lineno"> 480</tt>  <tt class="py-line"><tt class="py-docstring">        The folded fs assumes that information on which allele is ancestral or</tt> </tt>
<a name="L481"></a><tt class="py-lineno"> 481</tt>  <tt class="py-line"><tt class="py-docstring">        derived is unavailable. Thus the fs is in terms of minor allele </tt> </tt>
<a name="L482"></a><tt class="py-lineno"> 482</tt>  <tt class="py-line"><tt class="py-docstring">        frequency.  Note that this makes the fs into a "triangular" array.</tt> </tt>
<a name="L483"></a><tt class="py-lineno"> 483</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L484"></a><tt class="py-lineno"> 484</tt>  <tt class="py-line"><tt class="py-docstring">        Note that if a masked cell is folded into non-masked cell, the</tt> </tt>
<a name="L485"></a><tt class="py-lineno"> 485</tt>  <tt class="py-line"><tt class="py-docstring">        destination cell is masked as well.</tt> </tt>
<a name="L486"></a><tt class="py-lineno"> 486</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L487"></a><tt class="py-lineno"> 487</tt>  <tt class="py-line"><tt class="py-docstring">        Note also that folding is not done in-place. The return value is a new</tt> </tt>
<a name="L488"></a><tt class="py-lineno"> 488</tt>  <tt class="py-line"><tt class="py-docstring">        Spectrum object.</tt> </tt>
<a name="L489"></a><tt class="py-lineno"> 489</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L490"></a><tt class="py-lineno"> 490</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L491"></a><tt class="py-lineno"> 491</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Input Spectrum is already folded.'</tt><tt class="py-op">)</tt> </tt>
<a name="L492"></a><tt class="py-lineno"> 492</tt>  <tt class="py-line"> </tt>
<a name="L493"></a><tt class="py-lineno"> 493</tt>  <tt class="py-line">        <tt class="py-comment"># How many samples total do we have? The folded fs can only contain</tt> </tt>
<a name="L494"></a><tt class="py-lineno"> 494</tt>  <tt class="py-line">        <tt class="py-comment"># entries up to total_samples/2 (rounded down).</tt> </tt>
<a name="L495"></a><tt class="py-lineno"> 495</tt>  <tt class="py-line">        <tt class="py-name">total_samples</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-55', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">)</tt> </tt>
<a name="L496"></a><tt class="py-lineno"> 496</tt>  <tt class="py-line"> </tt>
<a name="L497"></a><tt class="py-lineno"> 497</tt>  <tt class="py-line">        <tt class="py-name">total_per_entry</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="dadi.Spectrum_mod.Spectrum._total_per_entry" class="py-name" href="#" onclick="return doclink('link-56', '_total_per_entry', 'link-10');">_total_per_entry</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L498"></a><tt class="py-lineno"> 498</tt>  <tt class="py-line">     </tt>
<a name="L499"></a><tt class="py-lineno"> 499</tt>  <tt class="py-line">        <tt class="py-comment"># Here's where we calculate which entries are nonsense in the folded fs.</tt> </tt>
<a name="L500"></a><tt class="py-lineno"> 500</tt>  <tt class="py-line">        <tt class="py-name">where_folded_out</tt> <tt class="py-op">=</tt> <tt class="py-name">total_per_entry</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">total_samples</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L501"></a><tt class="py-lineno"> 501</tt>  <tt class="py-line">     </tt>
<a name="L502"></a><tt class="py-lineno"> 502</tt>  <tt class="py-line">        <tt class="py-name">original_mask</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt> </tt>
<a name="L503"></a><tt class="py-lineno"> 503</tt>  <tt class="py-line">        <tt class="py-comment"># Here we create a mask that masks any values that were masked in</tt> </tt>
<a name="L504"></a><tt class="py-lineno"> 504</tt>  <tt class="py-line">        <tt class="py-comment"># the original fs (or folded onto by a masked value).</tt> </tt>
<a name="L505"></a><tt class="py-lineno"> 505</tt>  <tt class="py-line">        <tt class="py-name">final_mask</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_or</tt><tt class="py-op">(</tt><tt class="py-name">original_mask</tt><tt class="py-op">,</tt>  </tt>
<a name="L506"></a><tt class="py-lineno"> 506</tt>  <tt class="py-line">                                      <tt id="link-57" class="py-name"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-57', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">(</tt><tt class="py-name">original_mask</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L507"></a><tt class="py-lineno"> 507</tt>  <tt class="py-line">         </tt>
<a name="L508"></a><tt class="py-lineno"> 508</tt>  <tt class="py-line">        <tt class="py-comment"># To do the actual folding, we take those entries that would be folded</tt> </tt>
<a name="L509"></a><tt class="py-lineno"> 509</tt>  <tt class="py-line">        <tt class="py-comment"># out, reverse the array along all axes, and add them back to the</tt> </tt>
<a name="L510"></a><tt class="py-lineno"> 510</tt>  <tt class="py-line">        <tt class="py-comment"># original fs.</tt> </tt>
<a name="L511"></a><tt class="py-lineno"> 511</tt>  <tt class="py-line">        <tt class="py-name">reversed</tt> <tt class="py-op">=</tt> <tt id="link-58" class="py-name"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-58', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">(</tt><tt class="py-name">where_folded_out</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L512"></a><tt class="py-lineno"> 512</tt>  <tt class="py-line">        <tt class="py-name">folded</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_array</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">+</tt> <tt class="py-name">reversed</tt><tt class="py-op">)</tt> </tt>
<a name="L513"></a><tt class="py-lineno"> 513</tt>  <tt class="py-line">        <tt class="py-name">folded</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">where_folded_out</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L514"></a><tt class="py-lineno"> 514</tt>  <tt class="py-line">     </tt>
<a name="L515"></a><tt class="py-lineno"> 515</tt>  <tt class="py-line">        <tt class="py-comment"># Deal with those entries where assignment of the minor allele is</tt> </tt>
<a name="L516"></a><tt class="py-lineno"> 516</tt>  <tt class="py-line">        <tt class="py-comment"># ambiguous.</tt> </tt>
<a name="L517"></a><tt class="py-lineno"> 517</tt>  <tt class="py-line">        <tt class="py-name">where_ambiguous</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">total_per_entry</tt> <tt class="py-op">==</tt> <tt class="py-name">total_samples</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt><tt class="py-op">)</tt> </tt>
<a name="L518"></a><tt class="py-lineno"> 518</tt>  <tt class="py-line">        <tt class="py-name">ambiguous</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">(</tt><tt class="py-name">where_ambiguous</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno"> 519</tt>  <tt class="py-line">        <tt class="py-name">folded</tt> <tt class="py-op">+=</tt> <tt class="py-op">-</tt><tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-name">ambiguous</tt> <tt class="py-op">+</tt> <tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt id="link-59" class="py-name"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-59', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">(</tt><tt class="py-name">ambiguous</tt><tt class="py-op">)</tt> </tt>
<a name="L520"></a><tt class="py-lineno"> 520</tt>  <tt class="py-line">     </tt>
<a name="L521"></a><tt class="py-lineno"> 521</tt>  <tt class="py-line">        <tt class="py-comment"># Mask out the remains of the folding operation.</tt> </tt>
<a name="L522"></a><tt class="py-lineno"> 522</tt>  <tt class="py-line">        <tt class="py-name">final_mask</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_or</tt><tt class="py-op">(</tt><tt class="py-name">final_mask</tt><tt class="py-op">,</tt> <tt class="py-name">where_folded_out</tt><tt class="py-op">)</tt> </tt>
<a name="L523"></a><tt class="py-lineno"> 523</tt>  <tt class="py-line"> </tt>
<a name="L524"></a><tt class="py-lineno"> 524</tt>  <tt class="py-line">        <tt class="py-name">outfs</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-60', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">folded</tt><tt class="py-op">,</tt> <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">final_mask</tt><tt class="py-op">,</tt> <tt class="py-name">data_folded</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> </tt>
<a name="L525"></a><tt class="py-lineno"> 525</tt>  <tt class="py-line">                         <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L526"></a><tt class="py-lineno"> 526</tt>  <tt class="py-line">        <tt class="py-name">outfs</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> </tt>
<a name="L527"></a><tt class="py-lineno"> 527</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">outfs</tt> </tt>
</div><a name="L528"></a><tt class="py-lineno"> 528</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.unfold"></a><div id="Spectrum.unfold-def"><a name="L529"></a><tt class="py-lineno"> 529</tt> <a class="py-toggle" href="#" id="Spectrum.unfold-toggle" onclick="return toggle('Spectrum.unfold');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#unfold">unfold</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.unfold-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.unfold-expanded"><a name="L530"></a><tt class="py-lineno"> 530</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L531"></a><tt class="py-lineno"> 531</tt>  <tt class="py-line"><tt class="py-docstring">        Unfolded frequency spectrum</tt> </tt>
<a name="L532"></a><tt class="py-lineno"> 532</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L533"></a><tt class="py-lineno"> 533</tt>  <tt class="py-line"><tt class="py-docstring">        It is assumed that each state of a SNP is equally likely to be</tt> </tt>
<a name="L534"></a><tt class="py-lineno"> 534</tt>  <tt class="py-line"><tt class="py-docstring">        ancestral.</tt> </tt>
<a name="L535"></a><tt class="py-lineno"> 535</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L536"></a><tt class="py-lineno"> 536</tt>  <tt class="py-line"><tt class="py-docstring">        Note also that unfolding is not done in-place. The return value is a new</tt> </tt>
<a name="L537"></a><tt class="py-lineno"> 537</tt>  <tt class="py-line"><tt class="py-docstring">        Spectrum object.</tt> </tt>
<a name="L538"></a><tt class="py-lineno"> 538</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L539"></a><tt class="py-lineno"> 539</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L540"></a><tt class="py-lineno"> 540</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Input Spectrum is not folded.'</tt><tt class="py-op">)</tt> </tt>
<a name="L541"></a><tt class="py-lineno"> 541</tt>  <tt class="py-line"> </tt>
<a name="L542"></a><tt class="py-lineno"> 542</tt>  <tt class="py-line">        <tt class="py-comment"># Unfolding the data is easy.</tt> </tt>
<a name="L543"></a><tt class="py-lineno"> 543</tt>  <tt class="py-line">        <tt class="py-name">reversed_data</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-61', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
<a name="L544"></a><tt class="py-lineno"> 544</tt>  <tt class="py-line">        <tt class="py-name">newdata</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">+</tt> <tt class="py-name">reversed_data</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2.</tt> </tt>
<a name="L545"></a><tt class="py-lineno"> 545</tt>  <tt class="py-line"> </tt>
<a name="L546"></a><tt class="py-lineno"> 546</tt>  <tt class="py-line">        <tt class="py-comment"># Unfolding the mask is trickier. We want to preserve masking of entries</tt> </tt>
<a name="L547"></a><tt class="py-lineno"> 547</tt>  <tt class="py-line">        <tt class="py-comment"># that were masked in the original Spectrum.</tt> </tt>
<a name="L548"></a><tt class="py-lineno"> 548</tt>  <tt class="py-line">        <tt class="py-comment"># Which entries in the original Spectrum were masked solely because</tt> </tt>
<a name="L549"></a><tt class="py-lineno"> 549</tt>  <tt class="py-line">        <tt class="py-comment"># they are incompatible with a folded Spectrum?</tt> </tt>
<a name="L550"></a><tt class="py-lineno"> 550</tt>  <tt class="py-line">        <tt class="py-name">total_samples</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-62', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">)</tt> </tt>
<a name="L551"></a><tt class="py-lineno"> 551</tt>  <tt class="py-line">        <tt class="py-name">total_per_entry</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="dadi.Spectrum_mod.Spectrum._total_per_entry" class="py-name" href="#" onclick="return doclink('link-63', '_total_per_entry', 'link-10');">_total_per_entry</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L552"></a><tt class="py-lineno"> 552</tt>  <tt class="py-line">        <tt class="py-name">where_folded_out</tt> <tt class="py-op">=</tt> <tt class="py-name">total_per_entry</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">total_samples</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L553"></a><tt class="py-lineno"> 553</tt>  <tt class="py-line"> </tt>
<a name="L554"></a><tt class="py-lineno"> 554</tt>  <tt class="py-line">        <tt class="py-name">newmask</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_xor</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">,</tt> <tt class="py-name">where_folded_out</tt><tt class="py-op">)</tt> </tt>
<a name="L555"></a><tt class="py-lineno"> 555</tt>  <tt class="py-line">        <tt class="py-name">newmask</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_or</tt><tt class="py-op">(</tt><tt class="py-name">newmask</tt><tt class="py-op">,</tt> <tt id="link-64" class="py-name"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-64', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">(</tt><tt class="py-name">newmask</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L556"></a><tt class="py-lineno"> 556</tt>  <tt class="py-line">     </tt>
<a name="L557"></a><tt class="py-lineno"> 557</tt>  <tt class="py-line">        <tt class="py-name">outfs</tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-65', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">newdata</tt><tt class="py-op">,</tt> <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">newmask</tt><tt class="py-op">,</tt> <tt class="py-name">data_folded</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt>  </tt>
<a name="L558"></a><tt class="py-lineno"> 558</tt>  <tt class="py-line">                         <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L559"></a><tt class="py-lineno"> 559</tt>  <tt class="py-line">        <tt class="py-name">outfs</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> </tt>
<a name="L560"></a><tt class="py-lineno"> 560</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">outfs</tt> </tt>
</div><a name="L561"></a><tt class="py-lineno"> 561</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.fixed_size_sample"></a><div id="Spectrum.fixed_size_sample-def"><a name="L562"></a><tt class="py-lineno"> 562</tt> <a class="py-toggle" href="#" id="Spectrum.fixed_size_sample-toggle" onclick="return toggle('Spectrum.fixed_size_sample');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#fixed_size_sample">fixed_size_sample</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">nsamples</tt><tt class="py-op">,</tt> <tt class="py-param">only_nonmasked</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.fixed_size_sample-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.fixed_size_sample-expanded"><a name="L563"></a><tt class="py-lineno"> 563</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L564"></a><tt class="py-lineno"> 564</tt>  <tt class="py-line"><tt class="py-docstring">        Generate a resampled fs from the current one.</tt> </tt>
<a name="L565"></a><tt class="py-lineno"> 565</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L566"></a><tt class="py-lineno"> 566</tt>  <tt class="py-line"><tt class="py-docstring">        nsamples: Number of samples to include in the new FS.</tt> </tt>
<a name="L567"></a><tt class="py-lineno"> 567</tt>  <tt class="py-line"><tt class="py-docstring">        only_nonmasked: If True, only SNPs from non-masked will be resampled. </tt> </tt>
<a name="L568"></a><tt class="py-lineno"> 568</tt>  <tt class="py-line"><tt class="py-docstring">                        Otherwise, all SNPs will be used.</tt> </tt>
<a name="L569"></a><tt class="py-lineno"> 569</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L570"></a><tt class="py-lineno"> 570</tt>  <tt class="py-line">        <tt class="py-name">flat</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flatten</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L571"></a><tt class="py-lineno"> 571</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">only_nonmasked</tt><tt class="py-op">:</tt> </tt>
<a name="L572"></a><tt class="py-lineno"> 572</tt>  <tt class="py-line">            <tt class="py-name">pvals</tt> <tt class="py-op">=</tt> <tt class="py-name">flat</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">/</tt><tt class="py-name">flat</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L573"></a><tt class="py-lineno"> 573</tt>  <tt class="py-line">            <tt class="py-name">pvals</tt><tt class="py-op">[</tt><tt class="py-name">flat</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L574"></a><tt class="py-lineno"> 574</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L575"></a><tt class="py-lineno"> 575</tt>  <tt class="py-line">            <tt class="py-name">pvals</tt> <tt class="py-op">=</tt> <tt class="py-name">flat</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">/</tt><tt class="py-name">flat</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L576"></a><tt class="py-lineno"> 576</tt>  <tt class="py-line">     </tt>
<a name="L577"></a><tt class="py-lineno"> 577</tt>  <tt class="py-line">        <tt id="link-66" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.sample()=dadi.Spectrum_mod.Spectrum-class.html#sample"><a title="dadi.Spectrum_mod.Spectrum.sample" class="py-name" href="#" onclick="return doclink('link-66', 'sample', 'link-66');">sample</a></tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">random</tt><tt class="py-op">.</tt><tt class="py-name">multinomial</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">nsamples</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">pvals</tt><tt class="py-op">)</tt> </tt>
<a name="L578"></a><tt class="py-lineno"> 578</tt>  <tt class="py-line">        <tt id="link-67" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample" class="py-name" href="#" onclick="return doclink('link-67', 'sample', 'link-66');">sample</a></tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample" class="py-name" href="#" onclick="return doclink('link-68', 'sample', 'link-66');">sample</a></tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L579"></a><tt class="py-lineno"> 579</tt>  <tt class="py-line">     </tt>
<a name="L580"></a><tt class="py-lineno"> 580</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-69" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-69', 'dadi', 'link-2');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-70', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt id="link-71" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample" class="py-name" href="#" onclick="return doclink('link-71', 'sample', 'link-66');">sample</a></tt><tt class="py-op">,</tt> <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
</div><a name="L581"></a><tt class="py-lineno"> 581</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.sample"></a><div id="Spectrum.sample-def"><a name="L582"></a><tt class="py-lineno"> 582</tt> <a class="py-toggle" href="#" id="Spectrum.sample-toggle" onclick="return toggle('Spectrum.sample');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#sample">sample</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.sample-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.sample-expanded"><a name="L583"></a><tt class="py-lineno"> 583</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L584"></a><tt class="py-lineno"> 584</tt>  <tt class="py-line"><tt class="py-docstring">        Generate a Poisson-sampled fs from the current one.</tt> </tt>
<a name="L585"></a><tt class="py-lineno"> 585</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L586"></a><tt class="py-lineno"> 586</tt>  <tt class="py-line"><tt class="py-docstring">        Note: Entries where the current fs is masked or 0 will be masked in the</tt> </tt>
<a name="L587"></a><tt class="py-lineno"> 587</tt>  <tt class="py-line"><tt class="py-docstring">              output sampled fs.</tt> </tt>
<a name="L588"></a><tt class="py-lineno"> 588</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L589"></a><tt class="py-lineno"> 589</tt>  <tt class="py-line">        <tt class="py-keyword">import</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt> </tt>
<a name="L590"></a><tt class="py-lineno"> 590</tt>  <tt class="py-line">        <tt class="py-comment"># These are entries where the sampling has no meaning. Either the fs is</tt> </tt>
<a name="L591"></a><tt class="py-lineno"> 591</tt>  <tt class="py-line">        <tt class="py-comment"># 0 there or masked. </tt> </tt>
<a name="L592"></a><tt class="py-lineno"> 592</tt>  <tt class="py-line">        <tt class="py-name">bad_entries</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">logical_or</tt><tt class="py-op">(</tt><tt class="py-name">self</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">)</tt> </tt>
<a name="L593"></a><tt class="py-lineno"> 593</tt>  <tt class="py-line">        <tt class="py-comment"># We convert to a 1-d array for passing into the sampler</tt> </tt>
<a name="L594"></a><tt class="py-lineno"> 594</tt>  <tt class="py-line">        <tt class="py-name">means</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">copy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L595"></a><tt class="py-lineno"> 595</tt>  <tt class="py-line">        <tt class="py-comment"># Filter out those bad entries.</tt> </tt>
<a name="L596"></a><tt class="py-lineno"> 596</tt>  <tt class="py-line">        <tt class="py-name">means</tt><tt class="py-op">[</tt><tt class="py-name">bad_entries</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L597"></a><tt class="py-lineno"> 597</tt>  <tt class="py-line">        <tt class="py-comment"># Sample</tt> </tt>
<a name="L598"></a><tt class="py-lineno"> 598</tt>  <tt class="py-line">        <tt class="py-name">samp</tt> <tt class="py-op">=</tt> <tt class="py-name">scipy</tt><tt class="py-op">.</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">distributions</tt><tt class="py-op">.</tt><tt class="py-name">poisson</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-name">means</tt><tt class="py-op">,</tt> <tt class="py-name">size</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">means</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno"> 599</tt>  <tt class="py-line">        <tt class="py-comment"># Replace bad entries...</tt> </tt>
<a name="L600"></a><tt class="py-lineno"> 600</tt>  <tt class="py-line">        <tt class="py-name">samp</tt><tt class="py-op">[</tt><tt class="py-name">bad_entries</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L601"></a><tt class="py-lineno"> 601</tt>  <tt class="py-line">        <tt class="py-comment"># Convert back to a properly shaped array</tt> </tt>
<a name="L602"></a><tt class="py-lineno"> 602</tt>  <tt class="py-line">        <tt class="py-name">samp</tt> <tt class="py-op">=</tt> <tt class="py-name">samp</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L603"></a><tt class="py-lineno"> 603</tt>  <tt class="py-line">        <tt class="py-comment"># Convert to a fs and mask the bad entries</tt> </tt>
<a name="L604"></a><tt class="py-lineno"> 604</tt>  <tt class="py-line">        <tt class="py-name">samp</tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-72', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">samp</tt><tt class="py-op">,</tt> <tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-name">bad_entries</tt><tt class="py-op">,</tt> <tt class="py-name">data_folded</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">,</tt> </tt>
<a name="L605"></a><tt class="py-lineno"> 605</tt>  <tt class="py-line">                        <tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L606"></a><tt class="py-lineno"> 606</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">samp</tt> </tt>
</div><a name="L607"></a><tt class="py-lineno"> 607</tt>  <tt class="py-line"> </tt>
<a name="L608"></a><tt class="py-lineno"> 608</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum.from_ms_file"></a><div id="Spectrum.from_ms_file-def"><a name="L609"></a><tt class="py-lineno"> 609</tt> <a class="py-toggle" href="#" id="Spectrum.from_ms_file-toggle" onclick="return toggle('Spectrum.from_ms_file');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#from_ms_file">from_ms_file</a><tt class="py-op">(</tt><tt class="py-param">fid</tt><tt class="py-op">,</tt> <tt class="py-param">average</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-param">return_header</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
<a name="L610"></a><tt class="py-lineno"> 610</tt>  <tt class="py-line">                     <tt class="py-param">pop_assignments</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.from_ms_file-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.from_ms_file-expanded"><a name="L611"></a><tt class="py-lineno"> 611</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L612"></a><tt class="py-lineno"> 612</tt>  <tt class="py-line"><tt class="py-docstring">        Read frequency spectrum from file of ms output.</tt> </tt>
<a name="L613"></a><tt class="py-lineno"> 613</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L614"></a><tt class="py-lineno"> 614</tt>  <tt class="py-line"><tt class="py-docstring">        fid: string with file name to read from or an open file object.</tt> </tt>
<a name="L615"></a><tt class="py-lineno"> 615</tt>  <tt class="py-line"><tt class="py-docstring">        average: If True, the returned fs is the average over the runs in the ms</tt> </tt>
<a name="L616"></a><tt class="py-lineno"> 616</tt>  <tt class="py-line"><tt class="py-docstring">                 file. If False, the returned fs is the sum.</tt> </tt>
<a name="L617"></a><tt class="py-lineno"> 617</tt>  <tt class="py-line"><tt class="py-docstring">        mask_corners: If True, mask the 'absent in all samples' and 'fixed in</tt> </tt>
<a name="L618"></a><tt class="py-lineno"> 618</tt>  <tt class="py-line"><tt class="py-docstring">                      all samples' entries.</tt> </tt>
<a name="L619"></a><tt class="py-lineno"> 619</tt>  <tt class="py-line"><tt class="py-docstring">        return_header: If True, the return value is (fs, (command,seeds), where</tt> </tt>
<a name="L620"></a><tt class="py-lineno"> 620</tt>  <tt class="py-line"><tt class="py-docstring">                       command and seeds are strings containing the ms</tt> </tt>
<a name="L621"></a><tt class="py-lineno"> 621</tt>  <tt class="py-line"><tt class="py-docstring">                       commandline and the seeds used.</tt> </tt>
<a name="L622"></a><tt class="py-lineno"> 622</tt>  <tt class="py-line"><tt class="py-docstring">        pop_assignments: If None, the assignments of samples to populations is</tt> </tt>
<a name="L623"></a><tt class="py-lineno"> 623</tt>  <tt class="py-line"><tt class="py-docstring">                         done automatically, using the assignment in the ms</tt> </tt>
<a name="L624"></a><tt class="py-lineno"> 624</tt>  <tt class="py-line"><tt class="py-docstring">                         command line. To manually assign populations, pass a</tt> </tt>
<a name="L625"></a><tt class="py-lineno"> 625</tt>  <tt class="py-line"><tt class="py-docstring">                         list of the from [6,8]. This example places</tt> </tt>
<a name="L626"></a><tt class="py-lineno"> 626</tt>  <tt class="py-line"><tt class="py-docstring">                         the first 6 samples into population 1, and the next 8</tt> </tt>
<a name="L627"></a><tt class="py-lineno"> 627</tt>  <tt class="py-line"><tt class="py-docstring">                         into population 2.</tt> </tt>
<a name="L628"></a><tt class="py-lineno"> 628</tt>  <tt class="py-line"><tt class="py-docstring">        pop_ids: Optional list of strings containing the population labels.</tt> </tt>
<a name="L629"></a><tt class="py-lineno"> 629</tt>  <tt class="py-line"><tt class="py-docstring">                 If pop_ids is None, labels will be "pop0", "pop1", ...</tt> </tt>
<a name="L630"></a><tt class="py-lineno"> 630</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L631"></a><tt class="py-lineno"> 631</tt>  <tt class="py-line">        <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L632"></a><tt class="py-lineno"> 632</tt>  <tt class="py-line">        <tt class="py-comment"># Try to read from fid. If we can't, assume it's something that we can</tt> </tt>
<a name="L633"></a><tt class="py-lineno"> 633</tt>  <tt class="py-line">        <tt class="py-comment"># use to open a file.</tt> </tt>
<a name="L634"></a><tt class="py-lineno"> 634</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'read'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L635"></a><tt class="py-lineno"> 635</tt>  <tt class="py-line">            <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L636"></a><tt class="py-lineno"> 636</tt>  <tt class="py-line">            <tt class="py-name">fid</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L637"></a><tt class="py-lineno"> 637</tt>  <tt class="py-line"> </tt>
<a name="L638"></a><tt class="py-lineno"> 638</tt>  <tt class="py-line">        <tt class="py-comment"># Parse the commandline</tt> </tt>
<a name="L639"></a><tt class="py-lineno"> 639</tt>  <tt class="py-line">        <tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L640"></a><tt class="py-lineno"> 640</tt>  <tt class="py-line">        <tt class="py-name">command_terms</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L641"></a><tt class="py-lineno"> 641</tt>  <tt class="py-line">         </tt>
<a name="L642"></a><tt class="py-lineno"> 642</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">command_terms</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'ms'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L643"></a><tt class="py-lineno"> 643</tt>  <tt class="py-line">            <tt class="py-name">runs</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">command_terms</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L644"></a><tt class="py-lineno"> 644</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L645"></a><tt class="py-lineno"> 645</tt>  <tt class="py-line">                <tt class="py-name">pop_flag</tt> <tt class="py-op">=</tt> <tt class="py-name">command_terms</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-string">'-I'</tt><tt class="py-op">)</tt> </tt>
<a name="L646"></a><tt class="py-lineno"> 646</tt>  <tt class="py-line">                <tt class="py-name">num_pops</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">command_terms</tt><tt class="py-op">[</tt><tt class="py-name">pop_flag</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L647"></a><tt class="py-lineno"> 647</tt>  <tt class="py-line">                <tt class="py-name">pop_samples</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">command_terms</tt><tt class="py-op">[</tt><tt class="py-name">pop_flag</tt><tt class="py-op">+</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L648"></a><tt class="py-lineno"> 648</tt>  <tt class="py-line">                               <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">+</tt><tt class="py-name">num_pops</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L649"></a><tt class="py-lineno"> 649</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L650"></a><tt class="py-lineno"> 650</tt>  <tt class="py-line">                <tt class="py-name">num_pops</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L651"></a><tt class="py-lineno"> 651</tt>  <tt class="py-line">                <tt class="py-name">pop_samples</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">command_terms</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L652"></a><tt class="py-lineno"> 652</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L653"></a><tt class="py-lineno"> 653</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Unrecognized command string: %s.'</tt> <tt class="py-op">%</tt> <tt class="py-name">command</tt><tt class="py-op">)</tt> </tt>
<a name="L654"></a><tt class="py-lineno"> 654</tt>  <tt class="py-line">         </tt>
<a name="L655"></a><tt class="py-lineno"> 655</tt>  <tt class="py-line">        <tt class="py-name">total_samples</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">pop_samples</tt><tt class="py-op">)</tt> </tt>
<a name="L656"></a><tt class="py-lineno"> 656</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">pop_assignments</tt><tt class="py-op">:</tt> </tt>
<a name="L657"></a><tt class="py-lineno"> 657</tt>  <tt class="py-line">            <tt class="py-name">num_pops</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_assignments</tt><tt class="py-op">)</tt> </tt>
<a name="L658"></a><tt class="py-lineno"> 658</tt>  <tt class="py-line">            <tt class="py-name">pop_samples</tt> <tt class="py-op">=</tt> <tt class="py-name">pop_assignments</tt> </tt>
<a name="L659"></a><tt class="py-lineno"> 659</tt>  <tt class="py-line"> </tt>
<a name="L660"></a><tt class="py-lineno"> 660</tt>  <tt class="py-line">        <tt class="py-name">sample_indices</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">cumsum</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">pop_samples</tt><tt class="py-op">)</tt> </tt>
<a name="L661"></a><tt class="py-lineno"> 661</tt>  <tt class="py-line">        <tt class="py-name">bottom_l</tt> <tt class="py-op">=</tt> <tt class="py-name">sample_indices</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L662"></a><tt class="py-lineno"> 662</tt>  <tt class="py-line">        <tt class="py-name">top_l</tt> <tt class="py-op">=</tt> <tt class="py-name">sample_indices</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L663"></a><tt class="py-lineno"> 663</tt>  <tt class="py-line">         </tt>
<a name="L664"></a><tt class="py-lineno"> 664</tt>  <tt class="py-line">        <tt class="py-name">seeds</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L665"></a><tt class="py-lineno"> 665</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'//'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L666"></a><tt class="py-lineno"> 666</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L667"></a><tt class="py-lineno"> 667</tt>  <tt class="py-line">         </tt>
<a name="L668"></a><tt class="py-lineno"> 668</tt>  <tt class="py-line">        <tt class="py-name">counts</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_samples</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">int_</tt><tt class="py-op">)</tt> </tt>
<a name="L669"></a><tt class="py-lineno"> 669</tt>  <tt class="py-line">        <tt class="py-name">fs_shape</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">pop_samples</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L670"></a><tt class="py-lineno"> 670</tt>  <tt class="py-line">        <tt class="py-name">dimension</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">)</tt> </tt>
<a name="L671"></a><tt class="py-lineno"> 671</tt>  <tt class="py-line">         </tt>
<a name="L672"></a><tt class="py-lineno"> 672</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">dimension</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L673"></a><tt class="py-lineno"> 673</tt>  <tt class="py-line">            <tt class="py-name">bottom0</tt> <tt class="py-op">=</tt> <tt class="py-name">bottom_l</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L674"></a><tt class="py-lineno"> 674</tt>  <tt class="py-line">            <tt class="py-name">top0</tt> <tt class="py-op">=</tt> <tt class="py-name">top_l</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L675"></a><tt class="py-lineno"> 675</tt>  <tt class="py-line">            <tt class="py-name">bottom1</tt> <tt class="py-op">=</tt> <tt class="py-name">bottom_l</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L676"></a><tt class="py-lineno"> 676</tt>  <tt class="py-line">            <tt class="py-name">top1</tt> <tt class="py-op">=</tt> <tt class="py-name">top_l</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L677"></a><tt class="py-lineno"> 677</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">dimension</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L678"></a><tt class="py-lineno"> 678</tt>  <tt class="py-line">            <tt class="py-name">bottom2</tt> <tt class="py-op">=</tt> <tt class="py-name">bottom_l</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L679"></a><tt class="py-lineno"> 679</tt>  <tt class="py-line">            <tt class="py-name">top2</tt> <tt class="py-op">=</tt> <tt class="py-name">top_l</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L680"></a><tt class="py-lineno"> 680</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">dimension</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L681"></a><tt class="py-lineno"> 681</tt>  <tt class="py-line">            <tt class="py-name">bottom3</tt> <tt class="py-op">=</tt> <tt class="py-name">bottom_l</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L682"></a><tt class="py-lineno"> 682</tt>  <tt class="py-line">            <tt class="py-name">top3</tt> <tt class="py-op">=</tt> <tt class="py-name">top_l</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L683"></a><tt class="py-lineno"> 683</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">dimension</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L684"></a><tt class="py-lineno"> 684</tt>  <tt class="py-line">            <tt class="py-name">bottom4</tt> <tt class="py-op">=</tt> <tt class="py-name">bottom_l</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt>
<a name="L685"></a><tt class="py-lineno"> 685</tt>  <tt class="py-line">            <tt class="py-name">top4</tt> <tt class="py-op">=</tt> <tt class="py-name">top_l</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt>
<a name="L686"></a><tt class="py-lineno"> 686</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">dimension</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">5</tt><tt class="py-op">:</tt> </tt>
<a name="L687"></a><tt class="py-lineno"> 687</tt>  <tt class="py-line">            <tt class="py-name">bottom5</tt> <tt class="py-op">=</tt> <tt class="py-name">bottom_l</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L688"></a><tt class="py-lineno"> 688</tt>  <tt class="py-line">            <tt class="py-name">top5</tt> <tt class="py-op">=</tt> <tt class="py-name">top_l</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt>
<a name="L689"></a><tt class="py-lineno"> 689</tt>  <tt class="py-line">         </tt>
<a name="L690"></a><tt class="py-lineno"> 690</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">fs_shape</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">int_</tt><tt class="py-op">)</tt> </tt>
<a name="L691"></a><tt class="py-lineno"> 691</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">runs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L692"></a><tt class="py-lineno"> 692</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L693"></a><tt class="py-lineno"> 693</tt>  <tt class="py-line">            <tt class="py-name">segsites</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L694"></a><tt class="py-lineno"> 694</tt>  <tt class="py-line">             </tt>
<a name="L695"></a><tt class="py-lineno"> 695</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">segsites</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L696"></a><tt class="py-lineno"> 696</tt>  <tt class="py-line">                <tt class="py-comment"># Special case, need to read 3 lines to stay synced.</tt> </tt>
<a name="L697"></a><tt class="py-lineno"> 697</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L698"></a><tt class="py-lineno"> 698</tt>  <tt class="py-line">                    <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L699"></a><tt class="py-lineno"> 699</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L700"></a><tt class="py-lineno"> 700</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L701"></a><tt class="py-lineno"> 701</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'positions'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L702"></a><tt class="py-lineno"> 702</tt>  <tt class="py-line">                <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L703"></a><tt class="py-lineno"> 703</tt>  <tt class="py-line">         </tt>
<a name="L704"></a><tt class="py-lineno"> 704</tt>  <tt class="py-line">            <tt class="py-comment"># Read the chromosomes in</tt> </tt>
<a name="L705"></a><tt class="py-lineno"> 705</tt>  <tt class="py-line">            <tt class="py-name">chromos</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">segsites</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">total_samples</tt><tt class="py-op">)</tt> </tt>
<a name="L706"></a><tt class="py-lineno"> 706</tt>  <tt class="py-line">         </tt>
<a name="L707"></a><tt class="py-lineno"> 707</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">snp</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">segsites</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L708"></a><tt class="py-lineno"> 708</tt>  <tt class="py-line">                <tt class="py-comment"># Slice to get all the entries that refer to a particular SNP</tt> </tt>
<a name="L709"></a><tt class="py-lineno"> 709</tt>  <tt class="py-line">                <tt class="py-name">this_snp</tt> <tt class="py-op">=</tt> <tt class="py-name">chromos</tt><tt class="py-op">[</tt><tt class="py-name">snp</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-name">segsites</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L710"></a><tt class="py-lineno"> 710</tt>  <tt class="py-line">                <tt class="py-comment"># Count SNPs per population, and record them.</tt> </tt>
<a name="L711"></a><tt class="py-lineno"> 711</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">dimension</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L712"></a><tt class="py-lineno"> 712</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">this_snp</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L713"></a><tt class="py-lineno"> 713</tt>  <tt class="py-line">                <tt class="py-keyword">elif</tt> <tt class="py-name">dimension</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L714"></a><tt class="py-lineno"> 714</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom0</tt><tt class="py-op">:</tt><tt class="py-name">top0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L715"></a><tt class="py-lineno"> 715</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom1</tt><tt class="py-op">:</tt><tt class="py-name">top1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L716"></a><tt class="py-lineno"> 716</tt>  <tt class="py-line">                <tt class="py-keyword">elif</tt> <tt class="py-name">dimension</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L717"></a><tt class="py-lineno"> 717</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom0</tt><tt class="py-op">:</tt><tt class="py-name">top0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L718"></a><tt class="py-lineno"> 718</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom1</tt><tt class="py-op">:</tt><tt class="py-name">top1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L719"></a><tt class="py-lineno"> 719</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom2</tt><tt class="py-op">:</tt><tt class="py-name">top2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L720"></a><tt class="py-lineno"> 720</tt>  <tt class="py-line">                <tt class="py-keyword">elif</tt> <tt class="py-name">dimension</tt> <tt class="py-op">==</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L721"></a><tt class="py-lineno"> 721</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom0</tt><tt class="py-op">:</tt><tt class="py-name">top0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L722"></a><tt class="py-lineno"> 722</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom1</tt><tt class="py-op">:</tt><tt class="py-name">top1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L723"></a><tt class="py-lineno"> 723</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom2</tt><tt class="py-op">:</tt><tt class="py-name">top2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L724"></a><tt class="py-lineno"> 724</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom3</tt><tt class="py-op">:</tt><tt class="py-name">top3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L725"></a><tt class="py-lineno"> 725</tt>  <tt class="py-line">                <tt class="py-keyword">elif</tt> <tt class="py-name">dimension</tt> <tt class="py-op">==</tt> <tt class="py-number">5</tt><tt class="py-op">:</tt> </tt>
<a name="L726"></a><tt class="py-lineno"> 726</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom0</tt><tt class="py-op">:</tt><tt class="py-name">top0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L727"></a><tt class="py-lineno"> 727</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom1</tt><tt class="py-op">:</tt><tt class="py-name">top1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L728"></a><tt class="py-lineno"> 728</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom2</tt><tt class="py-op">:</tt><tt class="py-name">top2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L729"></a><tt class="py-lineno"> 729</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom3</tt><tt class="py-op">:</tt><tt class="py-name">top3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L730"></a><tt class="py-lineno"> 730</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom4</tt><tt class="py-op">:</tt><tt class="py-name">top4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L731"></a><tt class="py-lineno"> 731</tt>  <tt class="py-line">                <tt class="py-keyword">elif</tt> <tt class="py-name">dimension</tt> <tt class="py-op">==</tt> <tt class="py-number">6</tt><tt class="py-op">:</tt> </tt>
<a name="L732"></a><tt class="py-lineno"> 732</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom0</tt><tt class="py-op">:</tt><tt class="py-name">top0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L733"></a><tt class="py-lineno"> 733</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom1</tt><tt class="py-op">:</tt><tt class="py-name">top1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L734"></a><tt class="py-lineno"> 734</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom2</tt><tt class="py-op">:</tt><tt class="py-name">top2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L735"></a><tt class="py-lineno"> 735</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom3</tt><tt class="py-op">:</tt><tt class="py-name">top3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L736"></a><tt class="py-lineno"> 736</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom4</tt><tt class="py-op">:</tt><tt class="py-name">top4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L737"></a><tt class="py-lineno"> 737</tt>  <tt class="py-line">                         <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom5</tt><tt class="py-op">:</tt><tt class="py-name">top5</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L738"></a><tt class="py-lineno"> 738</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L739"></a><tt class="py-lineno"> 739</tt>  <tt class="py-line">                    <tt class="py-comment"># This is noticably slower, so we special case the cases</tt> </tt>
<a name="L740"></a><tt class="py-lineno"> 740</tt>  <tt class="py-line">                    <tt class="py-comment"># above.</tt> </tt>
<a name="L741"></a><tt class="py-lineno"> 741</tt>  <tt class="py-line">                    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">dimension</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L742"></a><tt class="py-lineno"> 742</tt>  <tt class="py-line">                        <tt class="py-name">bottom</tt> <tt class="py-op">=</tt> <tt class="py-name">bottom_l</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> </tt>
<a name="L743"></a><tt class="py-lineno"> 743</tt>  <tt class="py-line">                        <tt class="py-name">top</tt> <tt class="py-op">=</tt> <tt class="py-name">top_l</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> </tt>
<a name="L744"></a><tt class="py-lineno"> 744</tt>  <tt class="py-line">                        <tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">this_snp</tt><tt class="py-op">[</tt><tt class="py-name">bottom</tt><tt class="py-op">:</tt><tt class="py-name">top</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'1'</tt><tt class="py-op">)</tt> </tt>
<a name="L745"></a><tt class="py-lineno"> 745</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L746"></a><tt class="py-lineno"> 746</tt>  <tt class="py-line">         </tt>
<a name="L747"></a><tt class="py-lineno"> 747</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L748"></a><tt class="py-lineno"> 748</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L749"></a><tt class="py-lineno"> 749</tt>  <tt class="py-line"> </tt>
<a name="L750"></a><tt class="py-lineno"> 750</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">newfile</tt><tt class="py-op">:</tt> </tt>
<a name="L751"></a><tt class="py-lineno"> 751</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L752"></a><tt class="py-lineno"> 752</tt>  <tt class="py-line"> </tt>
<a name="L753"></a><tt class="py-lineno"> 753</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-73', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-74" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-74', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-75" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-75', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L754"></a><tt class="py-lineno"> 754</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">average</tt><tt class="py-op">:</tt> </tt>
<a name="L755"></a><tt class="py-lineno"> 755</tt>  <tt class="py-line">            <tt class="py-name">fs</tt> <tt class="py-op">/=</tt> <tt class="py-name">runs</tt> </tt>
<a name="L756"></a><tt class="py-lineno"> 756</tt>  <tt class="py-line"> </tt>
<a name="L757"></a><tt class="py-lineno"> 757</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">return_header</tt><tt class="py-op">:</tt> </tt>
<a name="L758"></a><tt class="py-lineno"> 758</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
<a name="L759"></a><tt class="py-lineno"> 759</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L760"></a><tt class="py-lineno"> 760</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">command</tt><tt class="py-op">,</tt><tt class="py-name">seeds</tt><tt class="py-op">)</tt> </tt>
</div><a name="L761"></a><tt class="py-lineno"> 761</tt>  <tt class="py-line"> </tt>
<a name="L762"></a><tt class="py-lineno"> 762</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum.from_sfscode_file"></a><div id="Spectrum.from_sfscode_file-def"><a name="L763"></a><tt class="py-lineno"> 763</tt> <a class="py-toggle" href="#" id="Spectrum.from_sfscode_file-toggle" onclick="return toggle('Spectrum.from_sfscode_file');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#from_sfscode_file">from_sfscode_file</a><tt class="py-op">(</tt><tt class="py-param">fid</tt><tt class="py-op">,</tt> <tt class="py-param">sites</tt><tt class="py-op">=</tt><tt class="py-string">'all'</tt><tt class="py-op">,</tt> <tt class="py-param">average</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L764"></a><tt class="py-lineno"> 764</tt>  <tt class="py-line">                          <tt class="py-param">return_header</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.from_sfscode_file-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.from_sfscode_file-expanded"><a name="L765"></a><tt class="py-lineno"> 765</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L766"></a><tt class="py-lineno"> 766</tt>  <tt class="py-line"><tt class="py-docstring">        Read frequency spectrum from file of sfs_code output.</tt> </tt>
<a name="L767"></a><tt class="py-lineno"> 767</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L768"></a><tt class="py-lineno"> 768</tt>  <tt class="py-line"><tt class="py-docstring">        fid: string with file name to read from or an open file object.</tt> </tt>
<a name="L769"></a><tt class="py-lineno"> 769</tt>  <tt class="py-line"><tt class="py-docstring">        sites: If sites=='all', return the fs of all sites. If sites == 'syn',</tt> </tt>
<a name="L770"></a><tt class="py-lineno"> 770</tt>  <tt class="py-line"><tt class="py-docstring">               use only synonymous mutations. If sites == 'nonsyn', use</tt> </tt>
<a name="L771"></a><tt class="py-lineno"> 771</tt>  <tt class="py-line"><tt class="py-docstring">               only non-synonymous mutations.</tt> </tt>
<a name="L772"></a><tt class="py-lineno"> 772</tt>  <tt class="py-line"><tt class="py-docstring">        average: If True, the returned fs is the average over the runs in the </tt> </tt>
<a name="L773"></a><tt class="py-lineno"> 773</tt>  <tt class="py-line"><tt class="py-docstring">                 file. If False, the returned fs is the sum.</tt> </tt>
<a name="L774"></a><tt class="py-lineno"> 774</tt>  <tt class="py-line"><tt class="py-docstring">        mask_corners: If True, mask the 'absent in all samples' and 'fixed in</tt> </tt>
<a name="L775"></a><tt class="py-lineno"> 775</tt>  <tt class="py-line"><tt class="py-docstring">                      all samples' entries.</tt> </tt>
<a name="L776"></a><tt class="py-lineno"> 776</tt>  <tt class="py-line"><tt class="py-docstring">        return_header: If true, the return value is (fs, (command,seeds), where</tt> </tt>
<a name="L777"></a><tt class="py-lineno"> 777</tt>  <tt class="py-line"><tt class="py-docstring">                       command and seeds are strings containing the ms</tt> </tt>
<a name="L778"></a><tt class="py-lineno"> 778</tt>  <tt class="py-line"><tt class="py-docstring">                       commandline and the seeds used.</tt> </tt>
<a name="L779"></a><tt class="py-lineno"> 779</tt>  <tt class="py-line"><tt class="py-docstring">        pop_ids: Optional list of strings containing the population labels.</tt> </tt>
<a name="L780"></a><tt class="py-lineno"> 780</tt>  <tt class="py-line"><tt class="py-docstring">                 If pop_ids is None, labels will be "pop0", "pop1", ...</tt> </tt>
<a name="L781"></a><tt class="py-lineno"> 781</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L782"></a><tt class="py-lineno"> 782</tt>  <tt class="py-line">        <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L783"></a><tt class="py-lineno"> 783</tt>  <tt class="py-line">        <tt class="py-comment"># Try to read from fid. If we can't, assume it's something that we can</tt> </tt>
<a name="L784"></a><tt class="py-lineno"> 784</tt>  <tt class="py-line">        <tt class="py-comment"># use to open a file.</tt> </tt>
<a name="L785"></a><tt class="py-lineno"> 785</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'read'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L786"></a><tt class="py-lineno"> 786</tt>  <tt class="py-line">            <tt class="py-name">newfile</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L787"></a><tt class="py-lineno"> 787</tt>  <tt class="py-line">            <tt class="py-name">fid</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">(</tt><tt class="py-name">fid</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L788"></a><tt class="py-lineno"> 788</tt>  <tt class="py-line"> </tt>
<a name="L789"></a><tt class="py-lineno"> 789</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">sites</tt> <tt class="py-op">==</tt> <tt class="py-string">'all'</tt><tt class="py-op">:</tt> </tt>
<a name="L790"></a><tt class="py-lineno"> 790</tt>  <tt class="py-line">            <tt class="py-name">only_nonsyn</tt><tt class="py-op">,</tt> <tt class="py-name">only_syn</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-name">False</tt> </tt>
<a name="L791"></a><tt class="py-lineno"> 791</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">sites</tt> <tt class="py-op">==</tt> <tt class="py-string">'syn'</tt><tt class="py-op">:</tt> </tt>
<a name="L792"></a><tt class="py-lineno"> 792</tt>  <tt class="py-line">            <tt class="py-name">only_nonsyn</tt><tt class="py-op">,</tt> <tt class="py-name">only_syn</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-name">True</tt> </tt>
<a name="L793"></a><tt class="py-lineno"> 793</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">sites</tt> <tt class="py-op">==</tt> <tt class="py-string">'nonsyn'</tt><tt class="py-op">:</tt> </tt>
<a name="L794"></a><tt class="py-lineno"> 794</tt>  <tt class="py-line">            <tt class="py-name">only_nonsyn</tt><tt class="py-op">,</tt> <tt class="py-name">only_syn</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt><tt class="py-op">,</tt> <tt class="py-name">False</tt> </tt>
<a name="L795"></a><tt class="py-lineno"> 795</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L796"></a><tt class="py-lineno"> 796</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"'sites' argument must be one of ('all', 'syn', "</tt> </tt>
<a name="L797"></a><tt class="py-lineno"> 797</tt>  <tt class="py-line">                             <tt class="py-string">"'nonsyn')."</tt><tt class="py-op">)</tt> </tt>
<a name="L798"></a><tt class="py-lineno"> 798</tt>  <tt class="py-line">         </tt>
<a name="L799"></a><tt class="py-lineno"> 799</tt>  <tt class="py-line">        <tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L800"></a><tt class="py-lineno"> 800</tt>  <tt class="py-line">        <tt class="py-name">command_terms</tt> <tt class="py-op">=</tt> <tt class="py-name">command</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L801"></a><tt class="py-lineno"> 801</tt>  <tt class="py-line">         </tt>
<a name="L802"></a><tt class="py-lineno"> 802</tt>  <tt class="py-line">        <tt class="py-name">runs</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">command_terms</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L803"></a><tt class="py-lineno"> 803</tt>  <tt class="py-line">        <tt class="py-name">num_pops</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">command_terms</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L804"></a><tt class="py-lineno"> 804</tt>  <tt class="py-line">         </tt>
<a name="L805"></a><tt class="py-lineno"> 805</tt>  <tt class="py-line">        <tt class="py-comment"># sfs_code default is 6 individuals, and I assume diploid pop</tt> </tt>
<a name="L806"></a><tt class="py-lineno"> 806</tt>  <tt class="py-line">        <tt class="py-name">pop_samples</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">12</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt>  <tt class="py-name">num_pops</tt> </tt>
<a name="L807"></a><tt class="py-lineno"> 807</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-string">'--sampSize'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">command_terms</tt> <tt class="py-keyword">or</tt> <tt class="py-string">'-n'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">command_terms</tt><tt class="py-op">:</tt> </tt>
<a name="L808"></a><tt class="py-lineno"> 808</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L809"></a><tt class="py-lineno"> 809</tt>  <tt class="py-line">                <tt class="py-name">pop_flag</tt> <tt class="py-op">=</tt> <tt class="py-name">command_terms</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-string">'--sampSize'</tt><tt class="py-op">)</tt> </tt>
<a name="L810"></a><tt class="py-lineno"> 810</tt>  <tt class="py-line">                <tt class="py-name">pop_flag</tt> <tt class="py-op">=</tt> <tt class="py-name">command_terms</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">(</tt><tt class="py-string">'-n'</tt><tt class="py-op">)</tt> </tt>
<a name="L811"></a><tt class="py-lineno"> 811</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L812"></a><tt class="py-lineno"> 812</tt>  <tt class="py-line">                <tt class="py-keyword">pass</tt> </tt>
<a name="L813"></a><tt class="py-lineno"> 813</tt>  <tt class="py-line">            <tt class="py-name">pop_samples</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">command_terms</tt><tt class="py-op">[</tt><tt class="py-name">pop_flag</tt><tt class="py-op">+</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L814"></a><tt class="py-lineno"> 814</tt>  <tt class="py-line">                           <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">+</tt><tt class="py-name">num_pops</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L815"></a><tt class="py-lineno"> 815</tt>  <tt class="py-line">         </tt>
<a name="L816"></a><tt class="py-lineno"> 816</tt>  <tt class="py-line">        <tt class="py-name">pop_samples</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">pop_samples</tt><tt class="py-op">)</tt> </tt>
<a name="L817"></a><tt class="py-lineno"> 817</tt>  <tt class="py-line">        <tt class="py-name">pop_digits</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">num_pops</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L818"></a><tt class="py-lineno"> 818</tt>  <tt class="py-line">        <tt class="py-name">pop_fixed_str</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">',%s.-1'</tt> <tt class="py-op">%</tt> <tt class="py-name">i</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">num_pops</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L819"></a><tt class="py-lineno"> 819</tt>  <tt class="py-line">        <tt class="py-name">pop_count_str</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">',%s.'</tt> <tt class="py-op">%</tt> <tt class="py-name">i</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">num_pops</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L820"></a><tt class="py-lineno"> 820</tt>  <tt class="py-line">         </tt>
<a name="L821"></a><tt class="py-lineno"> 821</tt>  <tt class="py-line">        <tt class="py-name">seeds</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L822"></a><tt class="py-lineno"> 822</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L823"></a><tt class="py-lineno"> 823</tt>  <tt class="py-line">         </tt>
<a name="L824"></a><tt class="py-lineno"> 824</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">pop_samples</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">int_</tt><tt class="py-op">)</tt> </tt>
<a name="L825"></a><tt class="py-lineno"> 825</tt>  <tt class="py-line">         </tt>
<a name="L826"></a><tt class="py-lineno"> 826</tt>  <tt class="py-line">        <tt class="py-comment"># line = //iteration...</tt> </tt>
<a name="L827"></a><tt class="py-lineno"> 827</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L828"></a><tt class="py-lineno"> 828</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">iter_ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">runs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L829"></a><tt class="py-lineno"> 829</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L830"></a><tt class="py-lineno"> 830</tt>  <tt class="py-line">                <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L831"></a><tt class="py-lineno"> 831</tt>  <tt class="py-line">         </tt>
<a name="L832"></a><tt class="py-lineno"> 832</tt>  <tt class="py-line">            <tt class="py-comment"># It is possible for a mutation to be listed several times in the</tt> </tt>
<a name="L833"></a><tt class="py-lineno"> 833</tt>  <tt class="py-line">            <tt class="py-comment"># output.  To accomodate this, I keep a dictionary of identities</tt> </tt>
<a name="L834"></a><tt class="py-lineno"> 834</tt>  <tt class="py-line">            <tt class="py-comment"># for those mutations, and hold off processing them until I've seen</tt> </tt>
<a name="L835"></a><tt class="py-lineno"> 835</tt>  <tt class="py-line">            <tt class="py-comment"># all mutations listed for the iteration.</tt> </tt>
<a name="L836"></a><tt class="py-lineno"> 836</tt>  <tt class="py-line">            <tt class="py-name">mut_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L837"></a><tt class="py-lineno"> 837</tt>  <tt class="py-line">             </tt>
<a name="L838"></a><tt class="py-lineno"> 838</tt>  <tt class="py-line">            <tt class="py-comment"># Loop until this iteration ends.</tt> </tt>
<a name="L839"></a><tt class="py-lineno"> 839</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'//'</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">line</tt> <tt class="py-op">!=</tt> <tt class="py-string">''</tt><tt class="py-op">:</tt> </tt>
<a name="L840"></a><tt class="py-lineno"> 840</tt>  <tt class="py-line">                <tt class="py-name">split_line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">';'</tt><tt class="py-op">)</tt> </tt>
<a name="L841"></a><tt class="py-lineno"> 841</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">split_line</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'\n'</tt><tt class="py-op">:</tt> </tt>
<a name="L842"></a><tt class="py-lineno"> 842</tt>  <tt class="py-line">                    <tt class="py-name">split_line</tt> <tt class="py-op">=</tt> <tt class="py-name">split_line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L843"></a><tt class="py-lineno"> 843</tt>  <tt class="py-line">         </tt>
<a name="L844"></a><tt class="py-lineno"> 844</tt>  <tt class="py-line">                <tt class="py-comment"># Loop over mutations on this line.</tt> </tt>
<a name="L845"></a><tt class="py-lineno"> 845</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">mut_ii</tt><tt class="py-op">,</tt> <tt class="py-name">mutation</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">split_line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L846"></a><tt class="py-lineno"> 846</tt>  <tt class="py-line">                    <tt class="py-name">counts_this_mut</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">num_pops</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">int_</tt><tt class="py-op">)</tt> </tt>
<a name="L847"></a><tt class="py-lineno"> 847</tt>  <tt class="py-line">         </tt>
<a name="L848"></a><tt class="py-lineno"> 848</tt>  <tt class="py-line">                    <tt class="py-name">split_mut</tt> <tt class="py-op">=</tt> <tt class="py-name">mutation</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">','</tt><tt class="py-op">)</tt> </tt>
<a name="L849"></a><tt class="py-lineno"> 849</tt>  <tt class="py-line">         </tt>
<a name="L850"></a><tt class="py-lineno"> 850</tt>  <tt class="py-line">                    <tt class="py-comment"># Exclude synonymous mutations</tt> </tt>
<a name="L851"></a><tt class="py-lineno"> 851</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">only_nonsyn</tt> <tt class="py-keyword">and</tt> <tt class="py-name">split_mut</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'0'</tt><tt class="py-op">:</tt> </tt>
<a name="L852"></a><tt class="py-lineno"> 852</tt>  <tt class="py-line">                        <tt class="py-keyword">continue</tt> </tt>
<a name="L853"></a><tt class="py-lineno"> 853</tt>  <tt class="py-line">                    <tt class="py-comment"># Exclude nonsynonymous mutations</tt> </tt>
<a name="L854"></a><tt class="py-lineno"> 854</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">only_syn</tt> <tt class="py-keyword">and</tt> <tt class="py-name">split_mut</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'1'</tt><tt class="py-op">:</tt> </tt>
<a name="L855"></a><tt class="py-lineno"> 855</tt>  <tt class="py-line">                        <tt class="py-keyword">continue</tt> </tt>
<a name="L856"></a><tt class="py-lineno"> 856</tt>  <tt class="py-line">         </tt>
<a name="L857"></a><tt class="py-lineno"> 857</tt>  <tt class="py-line">                    <tt class="py-name">ind_start</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-string">','</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">split_mut</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">12</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L858"></a><tt class="py-lineno"> 858</tt>  <tt class="py-line">                    <tt class="py-name">by_individual</tt> <tt class="py-op">=</tt> <tt class="py-name">mutation</tt><tt class="py-op">[</tt><tt class="py-name">ind_start</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L859"></a><tt class="py-lineno"> 859</tt>  <tt class="py-line">         </tt>
<a name="L860"></a><tt class="py-lineno"> 860</tt>  <tt class="py-line">                    <tt class="py-name">mut_id</tt> <tt class="py-op">=</tt> <tt class="py-string">','</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">split_mut</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">split_mut</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-number">11</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L861"></a><tt class="py-lineno"> 861</tt>  <tt class="py-line">         </tt>
<a name="L862"></a><tt class="py-lineno"> 862</tt>  <tt class="py-line">                    <tt class="py-comment"># Count mutations in each population</tt> </tt>
<a name="L863"></a><tt class="py-lineno"> 863</tt>  <tt class="py-line">                    <tt class="py-keyword">for</tt> <tt class="py-name">pop_ii</tt><tt class="py-op">,</tt><tt class="py-name">fixed_str</tt><tt class="py-op">,</tt><tt class="py-name">count_str</tt>\ </tt>
<a name="L864"></a><tt class="py-lineno"> 864</tt>  <tt class="py-line">                            <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">num_pops</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">pop_fixed_str</tt><tt class="py-op">,</tt>  </tt>
<a name="L865"></a><tt class="py-lineno"> 865</tt>  <tt class="py-line">                                   <tt class="py-name">pop_count_str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L866"></a><tt class="py-lineno"> 866</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-name">fixed_str</tt> <tt class="py-keyword">in</tt> <tt class="py-name">by_individual</tt><tt class="py-op">:</tt> </tt>
<a name="L867"></a><tt class="py-lineno"> 867</tt>  <tt class="py-line">                            <tt class="py-name">counts_this_mut</tt><tt class="py-op">[</tt><tt class="py-name">pop_ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">pop_samples</tt><tt class="py-op">[</tt><tt class="py-name">pop_ii</tt><tt class="py-op">]</tt> </tt>
<a name="L868"></a><tt class="py-lineno"> 868</tt>  <tt class="py-line">                        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L869"></a><tt class="py-lineno"> 869</tt>  <tt class="py-line">                            <tt class="py-name">counts_this_mut</tt><tt class="py-op">[</tt><tt class="py-name">pop_ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt>\ </tt>
<a name="L870"></a><tt class="py-lineno"> 870</tt>  <tt class="py-line">                                    <tt class="py-name">by_individual</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-name">count_str</tt><tt class="py-op">)</tt> </tt>
<a name="L871"></a><tt class="py-lineno"> 871</tt>  <tt class="py-line">         </tt>
<a name="L872"></a><tt class="py-lineno"> 872</tt>  <tt class="py-line">                    <tt class="py-comment"># Initialize the list that will track the counts for this</tt> </tt>
<a name="L873"></a><tt class="py-lineno"> 873</tt>  <tt class="py-line">                    <tt class="py-comment"># mutation. Using setdefault means that it won't overwrite</tt> </tt>
<a name="L874"></a><tt class="py-lineno"> 874</tt>  <tt class="py-line">                    <tt class="py-comment"># if there's already a list stored there.</tt> </tt>
<a name="L875"></a><tt class="py-lineno"> 875</tt>  <tt class="py-line">                    <tt class="py-name">mut_dict</tt><tt class="py-op">.</tt><tt class="py-name">setdefault</tt><tt class="py-op">(</tt><tt class="py-name">mut_id</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">num_pops</tt><tt class="py-op">)</tt> </tt>
<a name="L876"></a><tt class="py-lineno"> 876</tt>  <tt class="py-line">                    <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">num_pops</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L877"></a><tt class="py-lineno"> 877</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-name">counts_this_mut</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">mut_dict</tt><tt class="py-op">[</tt><tt class="py-name">mut_id</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L878"></a><tt class="py-lineno"> 878</tt>  <tt class="py-line">                            <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'Contradicting counts between '</tt> </tt>
<a name="L879"></a><tt class="py-lineno"> 879</tt>  <tt class="py-line">                                             <tt class="py-string">'listings for mutation %s in '</tt> </tt>
<a name="L880"></a><tt class="py-lineno"> 880</tt>  <tt class="py-line">                                             <tt class="py-string">'population %i.'</tt>  </tt>
<a name="L881"></a><tt class="py-lineno"> 881</tt>  <tt class="py-line">                                             <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">mut_id</tt><tt class="py-op">,</tt> <tt class="py-name">ii</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L882"></a><tt class="py-lineno"> 882</tt>  <tt class="py-line">                        <tt class="py-name">mut_dict</tt><tt class="py-op">[</tt><tt class="py-name">mut_id</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">counts_this_mut</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L883"></a><tt class="py-lineno"> 883</tt>  <tt class="py-line">                                                   <tt class="py-name">mut_dict</tt><tt class="py-op">[</tt><tt class="py-name">mut_id</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L884"></a><tt class="py-lineno"> 884</tt>  <tt class="py-line">         </tt>
<a name="L885"></a><tt class="py-lineno"> 885</tt>  <tt class="py-line">                <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L886"></a><tt class="py-lineno"> 886</tt>  <tt class="py-line">         </tt>
<a name="L887"></a><tt class="py-lineno"> 887</tt>  <tt class="py-line">            <tt class="py-comment"># Now apply all the mutations with fixations that we deffered.</tt> </tt>
<a name="L888"></a><tt class="py-lineno"> 888</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">mut_id</tt><tt class="py-op">,</tt> <tt class="py-name">counts</tt> <tt class="py-keyword">in</tt> <tt class="py-name">mut_dict</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L889"></a><tt class="py-lineno"> 889</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">pop_samples</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L890"></a><tt class="py-lineno"> 890</tt>  <tt class="py-line">                    <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'counts_this_mut &gt; pop_samples: %s &gt; '</tt> </tt>
<a name="L891"></a><tt class="py-lineno"> 891</tt>  <tt class="py-line">                                     <tt class="py-string">'%s\n%s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">,</tt> <tt class="py-name">pop_samples</tt><tt class="py-op">,</tt> <tt class="py-name">mut_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L892"></a><tt class="py-lineno"> 892</tt>  <tt class="py-line">                    <tt class="py-name">counts</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">,</tt> <tt class="py-name">pop_samples</tt><tt class="py-op">)</tt> </tt>
<a name="L893"></a><tt class="py-lineno"> 893</tt>  <tt class="py-line">                <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L894"></a><tt class="py-lineno"> 894</tt>  <tt class="py-line">         </tt>
<a name="L895"></a><tt class="py-lineno"> 895</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">newfile</tt><tt class="py-op">:</tt> </tt>
<a name="L896"></a><tt class="py-lineno"> 896</tt>  <tt class="py-line">            <tt class="py-name">fid</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L897"></a><tt class="py-lineno"> 897</tt>  <tt class="py-line">         </tt>
<a name="L898"></a><tt class="py-lineno"> 898</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-76', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-77" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-77', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-78" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-78', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L899"></a><tt class="py-lineno"> 899</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">average</tt><tt class="py-op">:</tt> </tt>
<a name="L900"></a><tt class="py-lineno"> 900</tt>  <tt class="py-line">            <tt class="py-name">fs</tt> <tt class="py-op">/=</tt> <tt class="py-name">runs</tt> </tt>
<a name="L901"></a><tt class="py-lineno"> 901</tt>  <tt class="py-line"> </tt>
<a name="L902"></a><tt class="py-lineno"> 902</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">return_header</tt><tt class="py-op">:</tt> </tt>
<a name="L903"></a><tt class="py-lineno"> 903</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
<a name="L904"></a><tt class="py-lineno"> 904</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L905"></a><tt class="py-lineno"> 905</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">command</tt><tt class="py-op">,</tt><tt class="py-name">seeds</tt><tt class="py-op">)</tt> </tt>
</div><a name="L906"></a><tt class="py-lineno"> 906</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.Fst"></a><div id="Spectrum.Fst-def"><a name="L907"></a><tt class="py-lineno"> 907</tt> <a class="py-toggle" href="#" id="Spectrum.Fst-toggle" onclick="return toggle('Spectrum.Fst');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#Fst">Fst</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.Fst-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.Fst-expanded"><a name="L908"></a><tt class="py-lineno"> 908</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L909"></a><tt class="py-lineno"> 909</tt>  <tt class="py-line"><tt class="py-docstring">        Wright's Fst between the populations represented in the fs.</tt> </tt>
<a name="L910"></a><tt class="py-lineno"> 910</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L911"></a><tt class="py-lineno"> 911</tt>  <tt class="py-line"><tt class="py-docstring">        This estimate of Fst assumes random mating, because we don't have</tt> </tt>
<a name="L912"></a><tt class="py-lineno"> 912</tt>  <tt class="py-line"><tt class="py-docstring">        heterozygote frequencies in the fs.</tt> </tt>
<a name="L913"></a><tt class="py-lineno"> 913</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L914"></a><tt class="py-lineno"> 914</tt>  <tt class="py-line"><tt class="py-docstring">        Calculation is by the method of Weir and Cockerham _Evolution_ 38:1358</tt> </tt>
<a name="L915"></a><tt class="py-lineno"> 915</tt>  <tt class="py-line"><tt class="py-docstring">        (1984).  For a single SNP, the relevant formula is at the top of page</tt> </tt>
<a name="L916"></a><tt class="py-lineno"> 916</tt>  <tt class="py-line"><tt class="py-docstring">        1363. To combine results between SNPs, we use the weighted average</tt> </tt>
<a name="L917"></a><tt class="py-lineno"> 917</tt>  <tt class="py-line"><tt class="py-docstring">        indicated by equation 10.</tt> </tt>
<a name="L918"></a><tt class="py-lineno"> 918</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L919"></a><tt class="py-lineno"> 919</tt>  <tt class="py-line">        <tt class="py-comment"># This gets a little obscure because we want to be able to work with</tt> </tt>
<a name="L920"></a><tt class="py-lineno"> 920</tt>  <tt class="py-line">        <tt class="py-comment"># spectra of arbitrary dimension.</tt> </tt>
<a name="L921"></a><tt class="py-lineno"> 921</tt>  <tt class="py-line">     </tt>
<a name="L922"></a><tt class="py-lineno"> 922</tt>  <tt class="py-line">        <tt class="py-comment"># First quantities from page 1360</tt> </tt>
<a name="L923"></a><tt class="py-lineno"> 923</tt>  <tt class="py-line">        <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-79', 'Npop', 'link-20');">Npop</a></tt> </tt>
<a name="L924"></a><tt class="py-lineno"> 924</tt>  <tt class="py-line">        <tt class="py-name">ns</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-80', 'sample_sizes', 'link-9');">sample_sizes</a></tt> </tt>
<a name="L925"></a><tt class="py-lineno"> 925</tt>  <tt class="py-line">        <tt class="py-name">nbar</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">mean</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt> </tt>
<a name="L926"></a><tt class="py-lineno"> 926</tt>  <tt class="py-line">        <tt class="py-name">nsum</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt> </tt>
<a name="L927"></a><tt class="py-lineno"> 927</tt>  <tt class="py-line">        <tt class="py-name">nc</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">nsum</tt> <tt class="py-op">-</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">nsum</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L928"></a><tt class="py-lineno"> 928</tt>  <tt class="py-line">     </tt>
<a name="L929"></a><tt class="py-lineno"> 929</tt>  <tt class="py-line">        <tt class="py-comment"># counts_per_pop is an r+1 dimensional array, where the last axis simply</tt> </tt>
<a name="L930"></a><tt class="py-lineno"> 930</tt>  <tt class="py-line">        <tt class="py-comment"># records the indices of the entry. </tt> </tt>
<a name="L931"></a><tt class="py-lineno"> 931</tt>  <tt class="py-line">        <tt class="py-comment"># For example, counts_per_pop[4,19,8] = [4,19,8]</tt> </tt>
<a name="L932"></a><tt class="py-lineno"> 932</tt>  <tt class="py-line">        <tt class="py-name">counts_per_pop</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">indices</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L933"></a><tt class="py-lineno"> 933</tt>  <tt class="py-line">        <tt class="py-name">counts_per_pop</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">transpose</tt><tt class="py-op">(</tt><tt class="py-name">counts_per_pop</tt><tt class="py-op">,</tt> <tt class="py-name">axes</tt><tt class="py-op">=</tt><tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">r</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L934"></a><tt class="py-lineno"> 934</tt>  <tt class="py-line">     </tt>
<a name="L935"></a><tt class="py-lineno"> 935</tt>  <tt class="py-line">        <tt class="py-comment"># The last axis of ptwiddle is now the relative frequency of SNPs in</tt> </tt>
<a name="L936"></a><tt class="py-lineno"> 936</tt>  <tt class="py-line">        <tt class="py-comment"># that bin in each of the populations.</tt> </tt>
<a name="L937"></a><tt class="py-lineno"> 937</tt>  <tt class="py-line">        <tt class="py-name">ptwiddle</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">*</tt><tt class="py-name">counts_per_pop</tt><tt class="py-op">/</tt><tt class="py-name">ns</tt> </tt>
<a name="L938"></a><tt class="py-lineno"> 938</tt>  <tt class="py-line">     </tt>
<a name="L939"></a><tt class="py-lineno"> 939</tt>  <tt class="py-line">        <tt class="py-comment"># Note that pbar is of the same shape as fs...</tt> </tt>
<a name="L940"></a><tt class="py-lineno"> 940</tt>  <tt class="py-line">        <tt class="py-name">pbar</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">*</tt><tt class="py-name">ptwiddle</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">nsum</tt> </tt>
<a name="L941"></a><tt class="py-lineno"> 941</tt>  <tt class="py-line">     </tt>
<a name="L942"></a><tt class="py-lineno"> 942</tt>  <tt class="py-line">        <tt class="py-comment"># We need to use 'this_slice' to get the proper aligment between</tt> </tt>
<a name="L943"></a><tt class="py-lineno"> 943</tt>  <tt class="py-line">        <tt class="py-comment"># ptwiddle and pbar.</tt> </tt>
<a name="L944"></a><tt class="py-lineno"> 944</tt>  <tt class="py-line">        <tt class="py-name">this_slice</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">r</tt> <tt class="py-op">+</tt> <tt class="py-op">[</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">newaxis</tt><tt class="py-op">]</tt> </tt>
<a name="L945"></a><tt class="py-lineno"> 945</tt>  <tt class="py-line">        <tt class="py-name">s2</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">ptwiddle</tt> <tt class="py-op">-</tt> <tt class="py-name">pbar</tt><tt class="py-op">[</tt><tt class="py-name">this_slice</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">nbar</tt><tt class="py-op">)</tt> </tt>
<a name="L946"></a><tt class="py-lineno"> 946</tt>  <tt class="py-line">     </tt>
<a name="L947"></a><tt class="py-lineno"> 947</tt>  <tt class="py-line">        <tt class="py-comment"># Note that this 'a' differs from equation 2, because we've used</tt> </tt>
<a name="L948"></a><tt class="py-lineno"> 948</tt>  <tt class="py-line">        <tt class="py-comment"># equation 3 and b = 0 to solve for hbar.</tt> </tt>
<a name="L949"></a><tt class="py-lineno"> 949</tt>  <tt class="py-line">        <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">nbar</tt><tt class="py-op">/</tt><tt class="py-name">nc</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">s2</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">nbar</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">pbar</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">pbar</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">r</tt><tt class="py-op">*</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L950"></a><tt class="py-lineno"> 950</tt>  <tt class="py-line">        <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">nbar</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">nbar</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">pbar</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">pbar</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">r</tt><tt class="py-op">*</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt> </tt>
<a name="L951"></a><tt class="py-lineno"> 951</tt>  <tt class="py-line">     </tt>
<a name="L952"></a><tt class="py-lineno"> 952</tt>  <tt class="py-line">        <tt class="py-comment"># The weighted sum over loci.</tt> </tt>
<a name="L953"></a><tt class="py-lineno"> 953</tt>  <tt class="py-line">        <tt class="py-name">asum</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt> <tt class="py-op">*</tt> <tt class="py-name">a</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L954"></a><tt class="py-lineno"> 954</tt>  <tt class="py-line">        <tt class="py-name">dsum</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt> <tt class="py-op">*</tt> <tt class="py-name">d</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L955"></a><tt class="py-lineno"> 955</tt>  <tt class="py-line">     </tt>
<a name="L956"></a><tt class="py-lineno"> 956</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">asum</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">asum</tt><tt class="py-op">+</tt><tt class="py-name">dsum</tt><tt class="py-op">)</tt> </tt>
</div><a name="L957"></a><tt class="py-lineno"> 957</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.S"></a><div id="Spectrum.S-def"><a name="L958"></a><tt class="py-lineno"> 958</tt> <a class="py-toggle" href="#" id="Spectrum.S-toggle" onclick="return toggle('Spectrum.S');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#S">S</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.S-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.S-expanded"><a name="L959"></a><tt class="py-lineno"> 959</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L960"></a><tt class="py-lineno"> 960</tt>  <tt class="py-line"><tt class="py-docstring">        Segregating sites.</tt> </tt>
<a name="L961"></a><tt class="py-lineno"> 961</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L962"></a><tt class="py-lineno"> 962</tt>  <tt class="py-line">        <tt class="py-name">oldmask</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">.</tt><tt class="py-name">copy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L963"></a><tt class="py-lineno"> 963</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-81', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L964"></a><tt class="py-lineno"> 964</tt>  <tt class="py-line">        <tt id="link-82" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.S()=dadi.Spectrum_mod.Spectrum-class.html#S"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-82', 'S', 'link-82');">S</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L965"></a><tt class="py-lineno"> 965</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt> <tt class="py-op">=</tt> <tt class="py-name">oldmask</tt> </tt>
<a name="L966"></a><tt class="py-lineno"> 966</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-83" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-83', 'S', 'link-82');">S</a></tt> </tt>
</div><a name="L967"></a><tt class="py-lineno"> 967</tt>  <tt class="py-line">     </tt>
<a name="Spectrum.Watterson_theta"></a><div id="Spectrum.Watterson_theta-def"><a name="L968"></a><tt class="py-lineno"> 968</tt> <a class="py-toggle" href="#" id="Spectrum.Watterson_theta-toggle" onclick="return toggle('Spectrum.Watterson_theta');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#Watterson_theta">Watterson_theta</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.Watterson_theta-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.Watterson_theta-expanded"><a name="L969"></a><tt class="py-lineno"> 969</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L970"></a><tt class="py-lineno"> 970</tt>  <tt class="py-line"><tt class="py-docstring">        Watterson's estimator of theta.</tt> </tt>
<a name="L971"></a><tt class="py-lineno"> 971</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L972"></a><tt class="py-lineno"> 972</tt>  <tt class="py-line"><tt class="py-docstring">        Note that is only sensible for 1-dimensional spectra.</tt> </tt>
<a name="L973"></a><tt class="py-lineno"> 973</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L974"></a><tt class="py-lineno"> 974</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-84', 'Npop', 'link-20');">Npop</a></tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L975"></a><tt class="py-lineno"> 975</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Only defined on a one-dimensional fs."</tt><tt class="py-op">)</tt> </tt>
<a name="L976"></a><tt class="py-lineno"> 976</tt>  <tt class="py-line">     </tt>
<a name="L977"></a><tt class="py-lineno"> 977</tt>  <tt class="py-line">        <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-85', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L978"></a><tt class="py-lineno"> 978</tt>  <tt class="py-line">        <tt id="link-86" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-86', 'S', 'link-82');">S</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-87', 'S', 'link-82');">S</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L979"></a><tt class="py-lineno"> 979</tt>  <tt class="py-line">        <tt class="py-name">denom</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L980"></a><tt class="py-lineno"> 980</tt>  <tt class="py-line">     </tt>
<a name="L981"></a><tt class="py-lineno"> 981</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-88" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-88', 'S', 'link-82');">S</a></tt><tt class="py-op">/</tt><tt class="py-name">denom</tt> </tt>
</div><a name="L982"></a><tt class="py-lineno"> 982</tt>  <tt class="py-line">     </tt>
<a name="Spectrum.pi"></a><div id="Spectrum.pi-def"><a name="L983"></a><tt class="py-lineno"> 983</tt> <a class="py-toggle" href="#" id="Spectrum.pi-toggle" onclick="return toggle('Spectrum.pi');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#pi">pi</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.pi-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.pi-expanded"><a name="L984"></a><tt class="py-lineno"> 984</tt>  <tt class="py-line">        <tt class="py-docstring">r"""</tt> </tt>
<a name="L985"></a><tt class="py-lineno"> 985</tt>  <tt class="py-line"><tt class="py-docstring">        Estimated expected number of pairwise differences between two</tt> </tt>
<a name="L986"></a><tt class="py-lineno"> 986</tt>  <tt class="py-line"><tt class="py-docstring">        chromosomes in the population.</tt> </tt>
<a name="L987"></a><tt class="py-lineno"> 987</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L988"></a><tt class="py-lineno"> 988</tt>  <tt class="py-line"><tt class="py-docstring">        Note that this estimate includes a factor of sample_size/(sample_size-1)</tt> </tt>
<a name="L989"></a><tt class="py-lineno"> 989</tt>  <tt class="py-line"><tt class="py-docstring">        to make E(\hat{pi}) = theta.</tt> </tt>
<a name="L990"></a><tt class="py-lineno"> 990</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L991"></a><tt class="py-lineno"> 991</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L992"></a><tt class="py-lineno"> 992</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Only defined for a one-dimensional SFS."</tt><tt class="py-op">)</tt> </tt>
<a name="L993"></a><tt class="py-lineno"> 993</tt>  <tt class="py-line">     </tt>
<a name="L994"></a><tt class="py-lineno"> 994</tt>  <tt class="py-line">        <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-89', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L995"></a><tt class="py-lineno"> 995</tt>  <tt class="py-line">        <tt class="py-comment"># sample frequencies p </tt> </tt>
<a name="L996"></a><tt class="py-lineno"> 996</tt>  <tt class="py-line">        <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">dtype</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">n</tt> </tt>
<a name="L997"></a><tt class="py-lineno"> 997</tt>  <tt class="py-line">        <tt class="py-comment"># This expression derives from Gillespie's _Population_Genetics:_A</tt> </tt>
<a name="L998"></a><tt class="py-lineno"> 998</tt>  <tt class="py-line">        <tt class="py-comment"># _Concise_Guide_, 2nd edition, section 2.6.</tt> </tt>
<a name="L999"></a><tt class="py-lineno"> 999</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">n</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-number">1.</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">*</tt><tt class="py-name">p</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1000"></a><tt class="py-lineno">1000</tt>  <tt class="py-line">     </tt>
<a name="Spectrum.Tajima_D"></a><div id="Spectrum.Tajima_D-def"><a name="L1001"></a><tt class="py-lineno">1001</tt> <a class="py-toggle" href="#" id="Spectrum.Tajima_D-toggle" onclick="return toggle('Spectrum.Tajima_D');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#Tajima_D">Tajima_D</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.Tajima_D-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.Tajima_D-expanded"><a name="L1002"></a><tt class="py-lineno">1002</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1003"></a><tt class="py-lineno">1003</tt>  <tt class="py-line"><tt class="py-docstring">        Tajima's D.</tt> </tt>
<a name="L1004"></a><tt class="py-lineno">1004</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L1005"></a><tt class="py-lineno">1005</tt>  <tt class="py-line"><tt class="py-docstring">        Following Gillespie "Population Genetics: A Concise Guide" pg. 45</tt> </tt>
<a name="L1006"></a><tt class="py-lineno">1006</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1007"></a><tt class="py-lineno">1007</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.Npop" class="py-name" href="#" onclick="return doclink('link-90', 'Npop', 'link-20');">Npop</a></tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L1008"></a><tt class="py-lineno">1008</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Only defined on a one-dimensional SFS."</tt><tt class="py-op">)</tt> </tt>
<a name="L1009"></a><tt class="py-lineno">1009</tt>  <tt class="py-line">     </tt>
<a name="L1010"></a><tt class="py-lineno">1010</tt>  <tt class="py-line">        <tt id="link-91" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-91', 'S', 'link-82');">S</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-92', 'S', 'link-82');">S</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1011"></a><tt class="py-lineno">1011</tt>  <tt class="py-line">     </tt>
<a name="L1012"></a><tt class="py-lineno">1012</tt>  <tt class="py-line">        <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-number">1.</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-93', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L1013"></a><tt class="py-lineno">1013</tt>  <tt class="py-line">        <tt class="py-name">pihat</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.pi()=dadi.Spectrum_mod.Spectrum-class.html#pi"><a title="dadi.Spectrum_mod.Spectrum.pi" class="py-name" href="#" onclick="return doclink('link-94', 'pi', 'link-94');">pi</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1014"></a><tt class="py-lineno">1014</tt>  <tt class="py-line">        <tt class="py-name">theta</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.Watterson_theta()=dadi.Spectrum_mod.Spectrum-class.html#Watterson_theta"><a title="dadi.Spectrum_mod.Spectrum.Watterson_theta" class="py-name" href="#" onclick="return doclink('link-95', 'Watterson_theta', 'link-95');">Watterson_theta</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1015"></a><tt class="py-lineno">1015</tt>  <tt class="py-line">     </tt>
<a name="L1016"></a><tt class="py-lineno">1016</tt>  <tt class="py-line">        <tt class="py-name">a1</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1017"></a><tt class="py-lineno">1017</tt>  <tt class="py-line">        <tt class="py-name">a2</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L1018"></a><tt class="py-lineno">1018</tt>  <tt class="py-line">        <tt class="py-name">b1</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1019"></a><tt class="py-lineno">1019</tt>  <tt class="py-line">        <tt class="py-name">b2</tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> <tt class="py-op">+</tt> <tt class="py-name">n</tt> <tt class="py-op">+</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">9</tt><tt class="py-op">*</tt><tt class="py-name">n</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1020"></a><tt class="py-lineno">1020</tt>  <tt class="py-line">        <tt class="py-name">c1</tt> <tt class="py-op">=</tt> <tt class="py-name">b1</tt> <tt class="py-op">-</tt> <tt class="py-number">1.</tt><tt class="py-op">/</tt><tt class="py-name">a1</tt> </tt>
<a name="L1021"></a><tt class="py-lineno">1021</tt>  <tt class="py-line">        <tt class="py-name">c2</tt> <tt class="py-op">=</tt> <tt class="py-name">b2</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">a1</tt><tt class="py-op">*</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">a2</tt><tt class="py-op">/</tt><tt class="py-name">a1</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L1022"></a><tt class="py-lineno">1022</tt>  <tt class="py-line">     </tt>
<a name="L1023"></a><tt class="py-lineno">1023</tt>  <tt class="py-line">        <tt class="py-name">C</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">c1</tt><tt class="py-op">/</tt><tt class="py-name">a1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt id="link-96" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-96', 'S', 'link-82');">S</a></tt> <tt class="py-op">+</tt> <tt class="py-name">c2</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">a1</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> <tt class="py-op">+</tt> <tt class="py-name">a2</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt id="link-97" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-97', 'S', 'link-82');">S</a></tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt id="link-98" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.S" class="py-name" href="#" onclick="return doclink('link-98', 'S', 'link-82');">S</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1024"></a><tt class="py-lineno">1024</tt>  <tt class="py-line">     </tt>
<a name="L1025"></a><tt class="py-lineno">1025</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">pihat</tt> <tt class="py-op">-</tt> <tt class="py-name">theta</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">C</tt> </tt>
</div><a name="L1026"></a><tt class="py-lineno">1026</tt>  <tt class="py-line"> </tt>
<a name="L1027"></a><tt class="py-lineno">1027</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._from_phi_1D_direct"></a><div id="Spectrum._from_phi_1D_direct-def"><a name="L1028"></a><tt class="py-lineno">1028</tt> <a class="py-toggle" href="#" id="Spectrum._from_phi_1D_direct-toggle" onclick="return toggle('Spectrum._from_phi_1D_direct');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_from_phi_1D_direct">_from_phi_1D_direct</a><tt class="py-op">(</tt><tt class="py-param">n</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> </tt>
<a name="L1029"></a><tt class="py-lineno">1029</tt>  <tt class="py-line">                            <tt class="py-param">het_ascertained</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._from_phi_1D_direct-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._from_phi_1D_direct-expanded"><a name="L1030"></a><tt class="py-lineno">1030</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1031"></a><tt class="py-lineno">1031</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1032"></a><tt class="py-lineno">1032</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1033"></a><tt class="py-lineno">1033</tt>  <tt class="py-line"><tt class="py-docstring">        See from_phi for explanation of arguments.</tt> </tt>
<a name="L1034"></a><tt class="py-lineno">1034</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1035"></a><tt class="py-lineno">1035</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1036"></a><tt class="py-lineno">1036</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1037"></a><tt class="py-lineno">1037</tt>  <tt class="py-line">            <tt class="py-name">factorx</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">xx</tt><tt class="py-op">**</tt><tt class="py-name">ii</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">)</tt> </tt>
<a name="L1038"></a><tt class="py-lineno">1038</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-op">==</tt> <tt class="py-string">'xx'</tt><tt class="py-op">:</tt> </tt>
<a name="L1039"></a><tt class="py-lineno">1039</tt>  <tt class="py-line">                <tt class="py-name">factorx</tt> <tt class="py-op">*=</tt> <tt class="py-name">xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1040"></a><tt class="py-lineno">1040</tt>  <tt class="py-line">            <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-99" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-99', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">factorx</tt> <tt class="py-op">*</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1041"></a><tt class="py-lineno">1041</tt>  <tt class="py-line">     </tt>
<a name="L1042"></a><tt class="py-lineno">1042</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-100" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-100', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-101" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-101', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-102" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-102', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L1043"></a><tt class="py-lineno">1043</tt>  <tt class="py-line"> </tt>
<a name="L1044"></a><tt class="py-lineno">1044</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._from_phi_1D_analytic"></a><div id="Spectrum._from_phi_1D_analytic-def"><a name="L1045"></a><tt class="py-lineno">1045</tt> <a class="py-toggle" href="#" id="Spectrum._from_phi_1D_analytic-toggle" onclick="return toggle('Spectrum._from_phi_1D_analytic');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_from_phi_1D_analytic">_from_phi_1D_analytic</a><tt class="py-op">(</tt><tt class="py-param">n</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L1046"></a><tt class="py-lineno">1046</tt>  <tt class="py-line">                              <tt class="py-param">divergent</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._from_phi_1D_analytic-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._from_phi_1D_analytic-expanded"><a name="L1047"></a><tt class="py-lineno">1047</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1048"></a><tt class="py-lineno">1048</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1049"></a><tt class="py-lineno">1049</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1050"></a><tt class="py-lineno">1050</tt>  <tt class="py-line"><tt class="py-docstring">        This function uses analytic formulae for integrating over a </tt> </tt>
<a name="L1051"></a><tt class="py-lineno">1051</tt>  <tt class="py-line"><tt class="py-docstring">        piecewise-linear approximation to phi.</tt> </tt>
<a name="L1052"></a><tt class="py-lineno">1052</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1053"></a><tt class="py-lineno">1053</tt>  <tt class="py-line"><tt class="py-docstring">        See from_phi for explanation of arguments.</tt> </tt>
<a name="L1054"></a><tt class="py-lineno">1054</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1055"></a><tt class="py-lineno">1055</tt>  <tt class="py-line"><tt class="py-docstring">        divergent: If True, the interval from xx[0] to xx[1] is modeled as</tt> </tt>
<a name="L1056"></a><tt class="py-lineno">1056</tt>  <tt class="py-line"><tt class="py-docstring">                   phi[1] * xx[1]/x. This captures the typical 1/x</tt> </tt>
<a name="L1057"></a><tt class="py-lineno">1057</tt>  <tt class="py-line"><tt class="py-docstring">                   divergence at x = 0.</tt> </tt>
<a name="L1058"></a><tt class="py-lineno">1058</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1059"></a><tt class="py-lineno">1059</tt>  <tt class="py-line">        <tt class="py-comment"># This function uses the result that </tt> </tt>
<a name="L1060"></a><tt class="py-lineno">1060</tt>  <tt class="py-line">        <tt class="py-comment"># \int_0^y \Gamma(a+b)/\Gamma(a) \Gamma(b) x^{a-1) (1-x)^{b-1} </tt> </tt>
<a name="L1061"></a><tt class="py-lineno">1061</tt>  <tt class="py-line">        <tt class="py-comment"># is betainc(a,b,y)</tt> </tt>
<a name="L1062"></a><tt class="py-lineno">1062</tt>  <tt class="py-line">        <tt class="py-comment"># So the integral in analytic for a piece-wise linear phi.</tt> </tt>
<a name="L1063"></a><tt class="py-lineno">1063</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1064"></a><tt class="py-lineno">1064</tt>  <tt class="py-line"> </tt>
<a name="L1065"></a><tt class="py-lineno">1065</tt>  <tt class="py-line">        <tt class="py-comment"># Values for xx just slighly (~1e-16) outside the range [0,1] can cause</tt> </tt>
<a name="L1066"></a><tt class="py-lineno">1066</tt>  <tt class="py-line">        <tt class="py-comment"># betainc calculation to fail.</tt> </tt>
<a name="L1067"></a><tt class="py-lineno">1067</tt>  <tt class="py-line">        <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">maximum</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L1068"></a><tt class="py-lineno">1068</tt>  <tt class="py-line"> </tt>
<a name="L1069"></a><tt class="py-lineno">1069</tt>  <tt class="py-line">        <tt class="py-comment"># Slopes of our linear-segments</tt> </tt>
<a name="L1070"></a><tt class="py-lineno">1070</tt>  <tt class="py-line">        <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1071"></a><tt class="py-lineno">1071</tt>  <tt class="py-line">        <tt class="py-comment"># For the integration of the "constant" term in the piecewise linear</tt> </tt>
<a name="L1072"></a><tt class="py-lineno">1072</tt>  <tt class="py-line">        <tt class="py-comment"># approximation of phi from each interval to the next.</tt> </tt>
<a name="L1073"></a><tt class="py-lineno">1073</tt>  <tt class="py-line">        <tt class="py-name">c1</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">s</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1074"></a><tt class="py-lineno">1074</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">d</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1075"></a><tt class="py-lineno">1075</tt>  <tt class="py-line">            <tt class="py-name">c2</tt> <tt class="py-op">=</tt> <tt class="py-name">s</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1076"></a><tt class="py-lineno">1076</tt>  <tt class="py-line">            <tt class="py-name">beta1</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-name">d</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1077"></a><tt class="py-lineno">1077</tt>  <tt class="py-line">            <tt class="py-name">beta2</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-name">d</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1078"></a><tt class="py-lineno">1078</tt>  <tt class="py-line">            <tt class="py-comment"># Each entry is the value of the integral from one value of xx to</tt> </tt>
<a name="L1079"></a><tt class="py-lineno">1079</tt>  <tt class="py-line">            <tt class="py-comment"># the next.</tt> </tt>
<a name="L1080"></a><tt class="py-lineno">1080</tt>  <tt class="py-line">            <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-name">c1</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta1</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta1</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">c2</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta2</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta2</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1081"></a><tt class="py-lineno">1081</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">divergent</tt><tt class="py-op">:</tt> </tt>
<a name="L1082"></a><tt class="py-lineno">1082</tt>  <tt class="py-line">                <tt class="py-name">entries</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-name">d</tt> <tt class="py-op">*</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-name">d</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1083"></a><tt class="py-lineno">1083</tt>  <tt class="py-line">            <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">d</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">entries</tt><tt class="py-op">)</tt> </tt>
<a name="L1084"></a><tt class="py-lineno">1084</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-103" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-103', 'dadi', 'link-2');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-104', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-105" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-105', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-106" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-106', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1085"></a><tt class="py-lineno">1085</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L1086"></a><tt class="py-lineno">1086</tt>  <tt class="py-line"> </tt>
<a name="L1087"></a><tt class="py-lineno">1087</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._from_phi_2D_direct"></a><div id="Spectrum._from_phi_2D_direct-def"><a name="L1088"></a><tt class="py-lineno">1088</tt> <a class="py-toggle" href="#" id="Spectrum._from_phi_2D_direct-toggle" onclick="return toggle('Spectrum._from_phi_2D_direct');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_from_phi_2D_direct">_from_phi_2D_direct</a><tt class="py-op">(</tt><tt class="py-param">nx</tt><tt class="py-op">,</tt> <tt class="py-param">ny</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">yy</tt><tt class="py-op">,</tt> <tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L1089"></a><tt class="py-lineno">1089</tt>  <tt class="py-line">                            <tt class="py-param">het_ascertained</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._from_phi_2D_direct-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._from_phi_2D_direct-expanded"><a name="L1090"></a><tt class="py-lineno">1090</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1091"></a><tt class="py-lineno">1091</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1092"></a><tt class="py-lineno">1092</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1093"></a><tt class="py-lineno">1093</tt>  <tt class="py-line"><tt class="py-docstring">        See from_phi for explanation of arguments.</tt> </tt>
<a name="L1094"></a><tt class="py-lineno">1094</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1095"></a><tt class="py-lineno">1095</tt>  <tt class="py-line">        <tt class="py-comment"># Calculate the 2D sfs from phi using the trapezoid rule for</tt> </tt>
<a name="L1096"></a><tt class="py-lineno">1096</tt>  <tt class="py-line">        <tt class="py-comment"># integration.</tt> </tt>
<a name="L1097"></a><tt class="py-lineno">1097</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1098"></a><tt class="py-lineno">1098</tt>  <tt class="py-line"> </tt>
<a name="L1099"></a><tt class="py-lineno">1099</tt>  <tt class="py-line">        <tt class="py-comment"># Cache to avoid duplicated work.</tt> </tt>
<a name="L1100"></a><tt class="py-lineno">1100</tt>  <tt class="py-line">        <tt class="py-name">factorx_cache</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1101"></a><tt class="py-lineno">1101</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1102"></a><tt class="py-lineno">1102</tt>  <tt class="py-line">            <tt class="py-name">factorx</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt> <tt class="py-name">ii</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">xx</tt><tt class="py-op">**</tt><tt class="py-name">ii</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">)</tt> </tt>
<a name="L1103"></a><tt class="py-lineno">1103</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-op">==</tt> <tt class="py-string">'xx'</tt><tt class="py-op">:</tt> </tt>
<a name="L1104"></a><tt class="py-lineno">1104</tt>  <tt class="py-line">                <tt class="py-name">factorx</tt> <tt class="py-op">*=</tt> <tt class="py-name">xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1105"></a><tt class="py-lineno">1105</tt>  <tt class="py-line">                <tt class="py-name">factorx_cache</tt><tt class="py-op">[</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">factorx</tt> </tt>
<a name="L1106"></a><tt class="py-lineno">1106</tt>  <tt class="py-line"> </tt>
<a name="L1107"></a><tt class="py-lineno">1107</tt>  <tt class="py-line">        <tt class="py-name">dx</tt><tt class="py-op">,</tt> <tt class="py-name">dy</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L1108"></a><tt class="py-lineno">1108</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1109"></a><tt class="py-lineno">1109</tt>  <tt class="py-line">            <tt class="py-name">factory</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">,</tt> <tt class="py-name">jj</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">yy</tt><tt class="py-op">**</tt><tt class="py-name">jj</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">)</tt> </tt>
<a name="L1110"></a><tt class="py-lineno">1110</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-op">==</tt> <tt class="py-string">'yy'</tt><tt class="py-op">:</tt> </tt>
<a name="L1111"></a><tt class="py-lineno">1111</tt>  <tt class="py-line">                <tt class="py-name">factory</tt> <tt class="py-op">*=</tt> <tt class="py-name">yy</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L1112"></a><tt class="py-lineno">1112</tt>  <tt class="py-line">                <tt class="py-name">integrated_over_y</tt> <tt class="py-op">=</tt> <tt id="link-107" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-107', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">factory</tt><tt class="py-op">[</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">newaxis</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dy</tt><tt class="py-op">)</tt> </tt>
<a name="L1113"></a><tt class="py-lineno">1113</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1114"></a><tt class="py-lineno">1114</tt>  <tt class="py-line">                    <tt class="py-name">factorx</tt> <tt class="py-op">=</tt> <tt class="py-name">factorx_cache</tt><tt class="py-op">[</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> </tt>
<a name="L1115"></a><tt class="py-lineno">1115</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-108" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-108', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">factorx</tt><tt class="py-op">*</tt><tt class="py-name">integrated_over_y</tt><tt class="py-op">,</tt> <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dx</tt><tt class="py-op">)</tt> </tt>
<a name="L1116"></a><tt class="py-lineno">1116</tt>  <tt class="py-line"> </tt>
<a name="L1117"></a><tt class="py-lineno">1117</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-109" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-109', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-110" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-110', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-111" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-111', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L1118"></a><tt class="py-lineno">1118</tt>  <tt class="py-line"> </tt>
<a name="L1119"></a><tt class="py-lineno">1119</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._from_phi_2D_admix_props"></a><div id="Spectrum._from_phi_2D_admix_props-def"><a name="L1120"></a><tt class="py-lineno">1120</tt> <a class="py-toggle" href="#" id="Spectrum._from_phi_2D_admix_props-toggle" onclick="return toggle('Spectrum._from_phi_2D_admix_props');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_from_phi_2D_admix_props">_from_phi_2D_admix_props</a><tt class="py-op">(</tt><tt class="py-param">nx</tt><tt class="py-op">,</tt> <tt class="py-param">ny</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">yy</tt><tt class="py-op">,</tt> <tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L1121"></a><tt class="py-lineno">1121</tt>  <tt class="py-line">                                 <tt class="py-param">admix_props</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._from_phi_2D_admix_props-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._from_phi_2D_admix_props-expanded"><a name="L1122"></a><tt class="py-lineno">1122</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1123"></a><tt class="py-lineno">1123</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1124"></a><tt class="py-lineno">1124</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1125"></a><tt class="py-lineno">1125</tt>  <tt class="py-line"><tt class="py-docstring">        See from_phi for explanation of arguments.</tt> </tt>
<a name="L1126"></a><tt class="py-lineno">1126</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1127"></a><tt class="py-lineno">1127</tt>  <tt class="py-line">        <tt class="py-name">xadmix</tt> <tt class="py-op">=</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L1128"></a><tt class="py-lineno">1128</tt>  <tt class="py-line">        <tt class="py-name">yadmix</tt> <tt class="py-op">=</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L1129"></a><tt class="py-lineno">1129</tt>  <tt class="py-line"> </tt>
<a name="L1130"></a><tt class="py-lineno">1130</tt>  <tt class="py-line">        <tt class="py-comment"># Calculate the 2D sfs from phi using the trapezoid rule for</tt> </tt>
<a name="L1131"></a><tt class="py-lineno">1131</tt>  <tt class="py-line">        <tt class="py-comment"># integration.</tt> </tt>
<a name="L1132"></a><tt class="py-lineno">1132</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1133"></a><tt class="py-lineno">1133</tt>  <tt class="py-line">         </tt>
<a name="L1134"></a><tt class="py-lineno">1134</tt>  <tt class="py-line">        <tt class="py-comment"># Cache to avoid duplicated work.</tt> </tt>
<a name="L1135"></a><tt class="py-lineno">1135</tt>  <tt class="py-line">        <tt class="py-name">factorx_cache</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1136"></a><tt class="py-lineno">1136</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1137"></a><tt class="py-lineno">1137</tt>  <tt class="py-line">            <tt class="py-name">factorx</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt> <tt class="py-name">ii</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">xadmix</tt><tt class="py-op">**</tt><tt class="py-name">ii</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xadmix</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">)</tt> </tt>
<a name="L1138"></a><tt class="py-lineno">1138</tt>  <tt class="py-line">            <tt class="py-name">factorx_cache</tt><tt class="py-op">[</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">factorx</tt> </tt>
<a name="L1139"></a><tt class="py-lineno">1139</tt>  <tt class="py-line">     </tt>
<a name="L1140"></a><tt class="py-lineno">1140</tt>  <tt class="py-line">        <tt class="py-name">dx</tt><tt class="py-op">,</tt> <tt class="py-name">dy</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L1141"></a><tt class="py-lineno">1141</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1142"></a><tt class="py-lineno">1142</tt>  <tt class="py-line">            <tt class="py-name">factory</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">,</tt> <tt class="py-name">jj</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">yadmix</tt><tt class="py-op">**</tt><tt class="py-name">jj</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">yadmix</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">)</tt> </tt>
<a name="L1143"></a><tt class="py-lineno">1143</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1144"></a><tt class="py-lineno">1144</tt>  <tt class="py-line">                <tt class="py-name">integrated_over_y</tt> <tt class="py-op">=</tt> <tt id="link-112" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-112', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">factorx_cache</tt><tt class="py-op">[</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">factory</tt> <tt class="py-op">*</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt> </tt>
<a name="L1145"></a><tt class="py-lineno">1145</tt>  <tt class="py-line">                                          <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dy</tt><tt class="py-op">)</tt> </tt>
<a name="L1146"></a><tt class="py-lineno">1146</tt>  <tt class="py-line">                <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-113" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-113', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">integrated_over_y</tt><tt class="py-op">,</tt> <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dx</tt><tt class="py-op">)</tt> </tt>
<a name="L1147"></a><tt class="py-lineno">1147</tt>  <tt class="py-line">     </tt>
<a name="L1148"></a><tt class="py-lineno">1148</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-114" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-114', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-115" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-115', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-116" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-116', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1149"></a><tt class="py-lineno">1149</tt>  <tt class="py-line">        <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1150"></a><tt class="py-lineno">1150</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L1151"></a><tt class="py-lineno">1151</tt>  <tt class="py-line"> </tt>
<a name="L1152"></a><tt class="py-lineno">1152</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._from_phi_2D_analytic"></a><div id="Spectrum._from_phi_2D_analytic-def"><a name="L1153"></a><tt class="py-lineno">1153</tt> <a class="py-toggle" href="#" id="Spectrum._from_phi_2D_analytic-toggle" onclick="return toggle('Spectrum._from_phi_2D_analytic');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_from_phi_2D_analytic">_from_phi_2D_analytic</a><tt class="py-op">(</tt><tt class="py-param">nx</tt><tt class="py-op">,</tt> <tt class="py-param">ny</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">yy</tt><tt class="py-op">,</tt> <tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._from_phi_2D_analytic-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._from_phi_2D_analytic-expanded"><a name="L1154"></a><tt class="py-lineno">1154</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1155"></a><tt class="py-lineno">1155</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1156"></a><tt class="py-lineno">1156</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1157"></a><tt class="py-lineno">1157</tt>  <tt class="py-line"><tt class="py-docstring">        This function uses analytic formulae for integrating over a </tt> </tt>
<a name="L1158"></a><tt class="py-lineno">1158</tt>  <tt class="py-line"><tt class="py-docstring">        piecewise-linear approximation to phi.</tt> </tt>
<a name="L1159"></a><tt class="py-lineno">1159</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1160"></a><tt class="py-lineno">1160</tt>  <tt class="py-line"><tt class="py-docstring">        See from_phi for explanation of arguments.</tt> </tt>
<a name="L1161"></a><tt class="py-lineno">1161</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1162"></a><tt class="py-lineno">1162</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1163"></a><tt class="py-lineno">1163</tt>  <tt class="py-line"> </tt>
<a name="L1164"></a><tt class="py-lineno">1164</tt>  <tt class="py-line">        <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">maximum</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L1165"></a><tt class="py-lineno">1165</tt>  <tt class="py-line">        <tt class="py-name">yy</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">maximum</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L1166"></a><tt class="py-lineno">1166</tt>  <tt class="py-line"> </tt>
<a name="L1167"></a><tt class="py-lineno">1167</tt>  <tt class="py-line">        <tt class="py-name">beta_cache_xx</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1168"></a><tt class="py-lineno">1168</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1169"></a><tt class="py-lineno">1169</tt>  <tt class="py-line">            <tt class="py-name">beta_cache_xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1170"></a><tt class="py-lineno">1170</tt>  <tt class="py-line">            <tt class="py-name">beta_cache_xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1171"></a><tt class="py-lineno">1171</tt>  <tt class="py-line"> </tt>
<a name="L1172"></a><tt class="py-lineno">1172</tt>  <tt class="py-line">        <tt class="py-name">s_yy</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1173"></a><tt class="py-lineno">1173</tt>  <tt class="py-line">        <tt class="py-name">c1_yy</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">s_yy</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1174"></a><tt class="py-lineno">1174</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1175"></a><tt class="py-lineno">1175</tt>  <tt class="py-line">            <tt class="py-name">c2_yy</tt> <tt class="py-op">=</tt> <tt class="py-name">s_yy</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1176"></a><tt class="py-lineno">1176</tt>  <tt class="py-line">            <tt class="py-name">beta1_yy</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L1177"></a><tt class="py-lineno">1177</tt>  <tt class="py-line">            <tt class="py-name">beta2_yy</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L1178"></a><tt class="py-lineno">1178</tt>  <tt class="py-line">            <tt class="py-name">over_y</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">c1_yy</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta1_yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta1_yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1179"></a><tt class="py-lineno">1179</tt>  <tt class="py-line">                               <tt class="py-op">+</tt> <tt class="py-name">c2_yy</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta2_yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta2_yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L1180"></a><tt class="py-lineno">1180</tt>  <tt class="py-line">                               <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1181"></a><tt class="py-lineno">1181</tt>  <tt class="py-line"> </tt>
<a name="L1182"></a><tt class="py-lineno">1182</tt>  <tt class="py-line">            <tt class="py-name">s_xx</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">over_y</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">over_y</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1183"></a><tt class="py-lineno">1183</tt>  <tt class="py-line">            <tt class="py-name">c1_xx</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">over_y</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">s_xx</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1184"></a><tt class="py-lineno">1184</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1185"></a><tt class="py-lineno">1185</tt>  <tt class="py-line">                <tt class="py-name">c2_xx</tt> <tt class="py-op">=</tt> <tt class="py-name">s_xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1186"></a><tt class="py-lineno">1186</tt>  <tt class="py-line">                <tt class="py-name">beta1_xx</tt> <tt class="py-op">=</tt> <tt class="py-name">beta_cache_xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1187"></a><tt class="py-lineno">1187</tt>  <tt class="py-line">                <tt class="py-name">beta2_xx</tt> <tt class="py-op">=</tt> <tt class="py-name">beta_cache_xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1188"></a><tt class="py-lineno">1188</tt>  <tt class="py-line">                <tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">c1_xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta1_xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta1_xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1189"></a><tt class="py-lineno">1189</tt>  <tt class="py-line">                                  <tt class="py-op">+</tt> <tt class="py-name">c2_xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta2_xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta2_xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1190"></a><tt class="py-lineno">1190</tt>  <tt class="py-line">                <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
<a name="L1191"></a><tt class="py-lineno">1191</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-117" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-117', 'dadi', 'link-2');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-118', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-119" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-119', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-120" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-120', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1192"></a><tt class="py-lineno">1192</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L1193"></a><tt class="py-lineno">1193</tt>  <tt class="py-line"> </tt>
<a name="L1194"></a><tt class="py-lineno">1194</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._from_phi_3D_direct"></a><div id="Spectrum._from_phi_3D_direct-def"><a name="L1195"></a><tt class="py-lineno">1195</tt> <a class="py-toggle" href="#" id="Spectrum._from_phi_3D_direct-toggle" onclick="return toggle('Spectrum._from_phi_3D_direct');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_from_phi_3D_direct">_from_phi_3D_direct</a><tt class="py-op">(</tt><tt class="py-param">nx</tt><tt class="py-op">,</tt> <tt class="py-param">ny</tt><tt class="py-op">,</tt> <tt class="py-param">nz</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">yy</tt><tt class="py-op">,</tt> <tt class="py-param">zz</tt><tt class="py-op">,</tt> <tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> </tt>
<a name="L1196"></a><tt class="py-lineno">1196</tt>  <tt class="py-line">                     <tt class="py-param">het_ascertained</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._from_phi_3D_direct-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._from_phi_3D_direct-expanded"><a name="L1197"></a><tt class="py-lineno">1197</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1198"></a><tt class="py-lineno">1198</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1199"></a><tt class="py-lineno">1199</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1200"></a><tt class="py-lineno">1200</tt>  <tt class="py-line"><tt class="py-docstring">        See from_phi for explanation of arguments.</tt> </tt>
<a name="L1201"></a><tt class="py-lineno">1201</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1202"></a><tt class="py-lineno">1202</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1203"></a><tt class="py-lineno">1203</tt>  <tt class="py-line">     </tt>
<a name="L1204"></a><tt class="py-lineno">1204</tt>  <tt class="py-line">        <tt class="py-name">dx</tt><tt class="py-op">,</tt> <tt class="py-name">dy</tt><tt class="py-op">,</tt> <tt class="py-name">dz</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt> </tt>
<a name="L1205"></a><tt class="py-lineno">1205</tt>  <tt class="py-line">        <tt class="py-name">half_dx</tt> <tt class="py-op">=</tt> <tt class="py-name">dx</tt><tt class="py-op">/</tt><tt class="py-number">2.0</tt> </tt>
<a name="L1206"></a><tt class="py-lineno">1206</tt>  <tt class="py-line">     </tt>
<a name="L1207"></a><tt class="py-lineno">1207</tt>  <tt class="py-line">        <tt class="py-comment"># We cache these calculations...</tt> </tt>
<a name="L1208"></a><tt class="py-lineno">1208</tt>  <tt class="py-line">        <tt class="py-name">factorx_cache</tt><tt class="py-op">,</tt> <tt class="py-name">factory_cache</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1209"></a><tt class="py-lineno">1209</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1210"></a><tt class="py-lineno">1210</tt>  <tt class="py-line">            <tt class="py-name">factorx</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt> <tt class="py-name">ii</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">xx</tt><tt class="py-op">**</tt><tt class="py-name">ii</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">)</tt> </tt>
<a name="L1211"></a><tt class="py-lineno">1211</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-op">==</tt> <tt class="py-string">'xx'</tt><tt class="py-op">:</tt> </tt>
<a name="L1212"></a><tt class="py-lineno">1212</tt>  <tt class="py-line">                <tt class="py-name">factorx</tt> <tt class="py-op">*=</tt> <tt class="py-name">xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1213"></a><tt class="py-lineno">1213</tt>  <tt class="py-line">            <tt class="py-name">factorx_cache</tt><tt class="py-op">[</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">factorx</tt> </tt>
<a name="L1214"></a><tt class="py-lineno">1214</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1215"></a><tt class="py-lineno">1215</tt>  <tt class="py-line">            <tt class="py-name">factory</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">,</tt> <tt class="py-name">jj</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">yy</tt><tt class="py-op">**</tt><tt class="py-name">jj</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">)</tt> </tt>
<a name="L1216"></a><tt class="py-lineno">1216</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-op">==</tt> <tt class="py-string">'yy'</tt><tt class="py-op">:</tt> </tt>
<a name="L1217"></a><tt class="py-lineno">1217</tt>  <tt class="py-line">                <tt class="py-name">factory</tt> <tt class="py-op">*=</tt> <tt class="py-name">yy</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L1218"></a><tt class="py-lineno">1218</tt>  <tt class="py-line">            <tt class="py-name">factory_cache</tt><tt class="py-op">[</tt><tt class="py-name">ny</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">factory</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L1219"></a><tt class="py-lineno">1219</tt>  <tt class="py-line">     </tt>
<a name="L1220"></a><tt class="py-lineno">1220</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">kk</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1221"></a><tt class="py-lineno">1221</tt>  <tt class="py-line">            <tt class="py-name">factorz</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">nz</tt><tt class="py-op">,</tt> <tt class="py-name">kk</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">zz</tt><tt class="py-op">**</tt><tt class="py-name">kk</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">nz</tt><tt class="py-op">-</tt><tt class="py-name">kk</tt><tt class="py-op">)</tt> </tt>
<a name="L1222"></a><tt class="py-lineno">1222</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-op">==</tt> <tt class="py-string">'zz'</tt><tt class="py-op">:</tt> </tt>
<a name="L1223"></a><tt class="py-lineno">1223</tt>  <tt class="py-line">                <tt class="py-name">factorz</tt> <tt class="py-op">*=</tt> <tt class="py-name">zz</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt> </tt>
<a name="L1224"></a><tt class="py-lineno">1224</tt>  <tt class="py-line">            <tt class="py-name">over_z</tt> <tt class="py-op">=</tt> <tt id="link-121" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-121', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">factorz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt> <tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dz</tt><tt class="py-op">)</tt> </tt>
<a name="L1225"></a><tt class="py-lineno">1225</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1226"></a><tt class="py-lineno">1226</tt>  <tt class="py-line">                <tt class="py-name">factory</tt> <tt class="py-op">=</tt> <tt class="py-name">factory_cache</tt><tt class="py-op">[</tt><tt class="py-name">ny</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> </tt>
<a name="L1227"></a><tt class="py-lineno">1227</tt>  <tt class="py-line">                <tt class="py-name">over_y</tt> <tt class="py-op">=</tt> <tt id="link-122" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-122', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">factory</tt> <tt class="py-op">*</tt> <tt class="py-name">over_z</tt><tt class="py-op">,</tt> <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dy</tt><tt class="py-op">)</tt> </tt>
<a name="L1228"></a><tt class="py-lineno">1228</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1229"></a><tt class="py-lineno">1229</tt>  <tt class="py-line">                    <tt class="py-name">factorx</tt> <tt class="py-op">=</tt> <tt class="py-name">factorx_cache</tt><tt class="py-op">[</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> </tt>
<a name="L1230"></a><tt class="py-lineno">1230</tt>  <tt class="py-line">                    <tt class="py-comment"># It's faster here to do the trapezoid rule explicitly</tt> </tt>
<a name="L1231"></a><tt class="py-lineno">1231</tt>  <tt class="py-line">                    <tt class="py-comment"># rather than using SciPy's more general routine.</tt> </tt>
<a name="L1232"></a><tt class="py-lineno">1232</tt>  <tt class="py-line">                    <tt class="py-name">integrand</tt> <tt class="py-op">=</tt> <tt class="py-name">factorx</tt> <tt class="py-op">*</tt> <tt class="py-name">over_y</tt> </tt>
<a name="L1233"></a><tt class="py-lineno">1233</tt>  <tt class="py-line">                    <tt class="py-name">ans</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">half_dx</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">integrand</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">integrand</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1234"></a><tt class="py-lineno">1234</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">ans</tt> </tt>
<a name="L1235"></a><tt class="py-lineno">1235</tt>  <tt class="py-line">     </tt>
<a name="L1236"></a><tt class="py-lineno">1236</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-123" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-123', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-124" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-124', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-125" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-125', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L1237"></a><tt class="py-lineno">1237</tt>  <tt class="py-line">     </tt>
<a name="L1238"></a><tt class="py-lineno">1238</tt>  <tt class="py-line"> </tt>
<a name="L1239"></a><tt class="py-lineno">1239</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._from_phi_3D_admix_props"></a><div id="Spectrum._from_phi_3D_admix_props-def"><a name="L1240"></a><tt class="py-lineno">1240</tt> <a class="py-toggle" href="#" id="Spectrum._from_phi_3D_admix_props-toggle" onclick="return toggle('Spectrum._from_phi_3D_admix_props');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_from_phi_3D_admix_props">_from_phi_3D_admix_props</a><tt class="py-op">(</tt><tt class="py-param">nx</tt><tt class="py-op">,</tt> <tt class="py-param">ny</tt><tt class="py-op">,</tt> <tt class="py-param">nz</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">yy</tt><tt class="py-op">,</tt> <tt class="py-param">zz</tt><tt class="py-op">,</tt> <tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> </tt>
<a name="L1241"></a><tt class="py-lineno">1241</tt>  <tt class="py-line">                                 <tt class="py-param">admix_props</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._from_phi_3D_admix_props-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._from_phi_3D_admix_props-expanded"><a name="L1242"></a><tt class="py-lineno">1242</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1243"></a><tt class="py-lineno">1243</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1244"></a><tt class="py-lineno">1244</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1245"></a><tt class="py-lineno">1245</tt>  <tt class="py-line"><tt class="py-docstring">        See from_phi for explanation of arguments.</tt> </tt>
<a name="L1246"></a><tt class="py-lineno">1246</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1247"></a><tt class="py-lineno">1247</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">admix_props</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L1248"></a><tt class="py-lineno">1248</tt>  <tt class="py-line">            <tt class="py-name">admix_props</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1249"></a><tt class="py-lineno">1249</tt>  <tt class="py-line"> </tt>
<a name="L1250"></a><tt class="py-lineno">1250</tt>  <tt class="py-line">        <tt class="py-name">xadmix</tt> <tt class="py-op">=</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1251"></a><tt class="py-lineno">1251</tt>  <tt class="py-line">                <tt class="py-op">+</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1252"></a><tt class="py-lineno">1252</tt>  <tt class="py-line">                <tt class="py-op">+</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L1253"></a><tt class="py-lineno">1253</tt>  <tt class="py-line">        <tt class="py-name">yadmix</tt> <tt class="py-op">=</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1254"></a><tt class="py-lineno">1254</tt>  <tt class="py-line">                <tt class="py-op">+</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1255"></a><tt class="py-lineno">1255</tt>  <tt class="py-line">                <tt class="py-op">+</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L1256"></a><tt class="py-lineno">1256</tt>  <tt class="py-line">        <tt class="py-name">zadmix</tt> <tt class="py-op">=</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1257"></a><tt class="py-lineno">1257</tt>  <tt class="py-line">                <tt class="py-op">+</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1258"></a><tt class="py-lineno">1258</tt>  <tt class="py-line">                <tt class="py-op">+</tt> <tt class="py-name">admix_props</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L1259"></a><tt class="py-lineno">1259</tt>  <tt class="py-line"> </tt>
<a name="L1260"></a><tt class="py-lineno">1260</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1261"></a><tt class="py-lineno">1261</tt>  <tt class="py-line">     </tt>
<a name="L1262"></a><tt class="py-lineno">1262</tt>  <tt class="py-line">        <tt class="py-name">dx</tt><tt class="py-op">,</tt> <tt class="py-name">dy</tt><tt class="py-op">,</tt> <tt class="py-name">dz</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt> </tt>
<a name="L1263"></a><tt class="py-lineno">1263</tt>  <tt class="py-line">        <tt class="py-name">half_dx</tt> <tt class="py-op">=</tt> <tt class="py-name">dx</tt><tt class="py-op">/</tt><tt class="py-number">2.0</tt> </tt>
<a name="L1264"></a><tt class="py-lineno">1264</tt>  <tt class="py-line">     </tt>
<a name="L1265"></a><tt class="py-lineno">1265</tt>  <tt class="py-line">        <tt class="py-comment"># We cache these calculations...</tt> </tt>
<a name="L1266"></a><tt class="py-lineno">1266</tt>  <tt class="py-line">        <tt class="py-name">factorx_cache</tt><tt class="py-op">,</tt> <tt class="py-name">factory_cache</tt><tt class="py-op">,</tt> <tt class="py-name">factorz_cache</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1267"></a><tt class="py-lineno">1267</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1268"></a><tt class="py-lineno">1268</tt>  <tt class="py-line">            <tt class="py-name">factorx</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt> <tt class="py-name">ii</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">xadmix</tt><tt class="py-op">**</tt><tt class="py-name">ii</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">xadmix</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">)</tt> </tt>
<a name="L1269"></a><tt class="py-lineno">1269</tt>  <tt class="py-line">            <tt class="py-name">factorx_cache</tt><tt class="py-op">[</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">factorx</tt> </tt>
<a name="L1270"></a><tt class="py-lineno">1270</tt>  <tt class="py-line"> </tt>
<a name="L1271"></a><tt class="py-lineno">1271</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1272"></a><tt class="py-lineno">1272</tt>  <tt class="py-line">            <tt class="py-name">factory</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">,</tt> <tt class="py-name">jj</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">yadmix</tt><tt class="py-op">**</tt><tt class="py-name">jj</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">yadmix</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">)</tt> </tt>
<a name="L1273"></a><tt class="py-lineno">1273</tt>  <tt class="py-line">            <tt class="py-name">factory_cache</tt><tt class="py-op">[</tt><tt class="py-name">ny</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">factory</tt> </tt>
<a name="L1274"></a><tt class="py-lineno">1274</tt>  <tt class="py-line"> </tt>
<a name="L1275"></a><tt class="py-lineno">1275</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">kk</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1276"></a><tt class="py-lineno">1276</tt>  <tt class="py-line">            <tt class="py-name">factorz</tt> <tt class="py-op">=</tt> <tt class="py-name">comb</tt><tt class="py-op">(</tt><tt class="py-name">nz</tt><tt class="py-op">,</tt> <tt class="py-name">kk</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">zadmix</tt><tt class="py-op">**</tt><tt class="py-name">kk</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">zadmix</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">nz</tt><tt class="py-op">-</tt><tt class="py-name">kk</tt><tt class="py-op">)</tt> </tt>
<a name="L1277"></a><tt class="py-lineno">1277</tt>  <tt class="py-line">            <tt class="py-name">factorz_cache</tt><tt class="py-op">[</tt><tt class="py-name">nz</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">factorz</tt> </tt>
<a name="L1278"></a><tt class="py-lineno">1278</tt>  <tt class="py-line">     </tt>
<a name="L1279"></a><tt class="py-lineno">1279</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">kk</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1280"></a><tt class="py-lineno">1280</tt>  <tt class="py-line">            <tt class="py-name">factorz</tt> <tt class="py-op">=</tt> <tt class="py-name">factorz_cache</tt><tt class="py-op">[</tt><tt class="py-name">nz</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> </tt>
<a name="L1281"></a><tt class="py-lineno">1281</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1282"></a><tt class="py-lineno">1282</tt>  <tt class="py-line">                <tt class="py-name">factory</tt> <tt class="py-op">=</tt> <tt class="py-name">factory_cache</tt><tt class="py-op">[</tt><tt class="py-name">ny</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">]</tt> </tt>
<a name="L1283"></a><tt class="py-lineno">1283</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1284"></a><tt class="py-lineno">1284</tt>  <tt class="py-line">                    <tt class="py-name">factorx</tt> <tt class="py-op">=</tt> <tt class="py-name">factorx_cache</tt><tt class="py-op">[</tt><tt class="py-name">nx</tt><tt class="py-op">,</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> </tt>
<a name="L1285"></a><tt class="py-lineno">1285</tt>  <tt class="py-line">                    <tt class="py-name">over_z</tt> <tt class="py-op">=</tt> <tt id="link-126" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-126', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">factorz</tt> <tt class="py-op">*</tt> <tt class="py-name">factory</tt> <tt class="py-op">*</tt> <tt class="py-name">factorx</tt> <tt class="py-op">*</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dz</tt><tt class="py-op">)</tt> </tt>
<a name="L1286"></a><tt class="py-lineno">1286</tt>  <tt class="py-line">                    <tt class="py-name">over_y</tt> <tt class="py-op">=</tt> <tt id="link-127" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-127', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">over_z</tt><tt class="py-op">,</tt> <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dy</tt><tt class="py-op">)</tt> </tt>
<a name="L1287"></a><tt class="py-lineno">1287</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-128" class="py-name"><a title="dadi.Numerics.trapz" class="py-name" href="#" onclick="return doclink('link-128', 'trapz', 'link-1');">trapz</a></tt><tt class="py-op">(</tt><tt class="py-name">over_y</tt><tt class="py-op">,</tt> <tt class="py-name">dx</tt><tt class="py-op">=</tt><tt class="py-name">dx</tt><tt class="py-op">)</tt> </tt>
<a name="L1288"></a><tt class="py-lineno">1288</tt>  <tt class="py-line">     </tt>
<a name="L1289"></a><tt class="py-lineno">1289</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-129" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-129', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-130" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-130', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-131" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-131', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L1290"></a><tt class="py-lineno">1290</tt>  <tt class="py-line"> </tt>
<a name="L1291"></a><tt class="py-lineno">1291</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._from_phi_3D_analytic"></a><div id="Spectrum._from_phi_3D_analytic-def"><a name="L1292"></a><tt class="py-lineno">1292</tt> <a class="py-toggle" href="#" id="Spectrum._from_phi_3D_analytic-toggle" onclick="return toggle('Spectrum._from_phi_3D_analytic');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_from_phi_3D_analytic">_from_phi_3D_analytic</a><tt class="py-op">(</tt><tt class="py-param">nx</tt><tt class="py-op">,</tt> <tt class="py-param">ny</tt><tt class="py-op">,</tt> <tt class="py-param">nz</tt><tt class="py-op">,</tt> <tt class="py-param">xx</tt><tt class="py-op">,</tt> <tt class="py-param">yy</tt><tt class="py-op">,</tt> <tt class="py-param">zz</tt><tt class="py-op">,</tt> <tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._from_phi_3D_analytic-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._from_phi_3D_analytic-expanded"><a name="L1293"></a><tt class="py-lineno">1293</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1294"></a><tt class="py-lineno">1294</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1295"></a><tt class="py-lineno">1295</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1296"></a><tt class="py-lineno">1296</tt>  <tt class="py-line"><tt class="py-docstring">        This function uses analytic formulae for integrating over a </tt> </tt>
<a name="L1297"></a><tt class="py-lineno">1297</tt>  <tt class="py-line"><tt class="py-docstring">        piecewise-linear approximation to phi.</tt> </tt>
<a name="L1298"></a><tt class="py-lineno">1298</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1299"></a><tt class="py-lineno">1299</tt>  <tt class="py-line"><tt class="py-docstring">        See from_phi for explanation of arguments.</tt> </tt>
<a name="L1300"></a><tt class="py-lineno">1300</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1301"></a><tt class="py-lineno">1301</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1302"></a><tt class="py-lineno">1302</tt>  <tt class="py-line"> </tt>
<a name="L1303"></a><tt class="py-lineno">1303</tt>  <tt class="py-line">        <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">maximum</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L1304"></a><tt class="py-lineno">1304</tt>  <tt class="py-line">        <tt class="py-name">yy</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">maximum</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L1305"></a><tt class="py-lineno">1305</tt>  <tt class="py-line">        <tt class="py-name">zz</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">maximum</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L1306"></a><tt class="py-lineno">1306</tt>  <tt class="py-line"> </tt>
<a name="L1307"></a><tt class="py-lineno">1307</tt>  <tt class="py-line">        <tt class="py-name">beta_cache_xx</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1308"></a><tt class="py-lineno">1308</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1309"></a><tt class="py-lineno">1309</tt>  <tt class="py-line">            <tt class="py-name">beta_cache_xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1310"></a><tt class="py-lineno">1310</tt>  <tt class="py-line">            <tt class="py-name">beta_cache_xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L1311"></a><tt class="py-lineno">1311</tt>  <tt class="py-line">        <tt class="py-name">beta_cache_yy</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1312"></a><tt class="py-lineno">1312</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1313"></a><tt class="py-lineno">1313</tt>  <tt class="py-line">            <tt class="py-name">beta_cache_yy</tt><tt class="py-op">[</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L1314"></a><tt class="py-lineno">1314</tt>  <tt class="py-line">            <tt class="py-name">beta_cache_yy</tt><tt class="py-op">[</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">yy</tt><tt class="py-op">)</tt> </tt>
<a name="L1315"></a><tt class="py-lineno">1315</tt>  <tt class="py-line"> </tt>
<a name="L1316"></a><tt class="py-lineno">1316</tt>  <tt class="py-line">        <tt class="py-name">s_zz</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1317"></a><tt class="py-lineno">1317</tt>  <tt class="py-line">        <tt class="py-name">c1_zz</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">s_zz</tt><tt class="py-op">*</tt><tt class="py-name">zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1318"></a><tt class="py-lineno">1318</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">kk</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1319"></a><tt class="py-lineno">1319</tt>  <tt class="py-line">            <tt class="py-name">c2_zz</tt> <tt class="py-op">=</tt> <tt class="py-name">s_zz</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">nz</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1320"></a><tt class="py-lineno">1320</tt>  <tt class="py-line">            <tt class="py-name">beta1_zz</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">nz</tt><tt class="py-op">-</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt> </tt>
<a name="L1321"></a><tt class="py-lineno">1321</tt>  <tt class="py-line">            <tt class="py-name">beta2_zz</tt> <tt class="py-op">=</tt> <tt class="py-name">betainc</tt><tt class="py-op">(</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nz</tt><tt class="py-op">-</tt><tt class="py-name">kk</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">zz</tt><tt class="py-op">)</tt> </tt>
<a name="L1322"></a><tt class="py-lineno">1322</tt>  <tt class="py-line">            <tt class="py-name">over_z</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">c1_zz</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta1_zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta1_zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">c2_zz</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta2_zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta2_zz</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1323"></a><tt class="py-lineno">1323</tt>  <tt class="py-line"> </tt>
<a name="L1324"></a><tt class="py-lineno">1324</tt>  <tt class="py-line">            <tt class="py-name">s_yy</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">over_z</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">over_z</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1325"></a><tt class="py-lineno">1325</tt>  <tt class="py-line">            <tt class="py-name">c1_yy</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">over_z</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">s_yy</tt><tt class="py-op">*</tt><tt class="py-name">yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1326"></a><tt class="py-lineno">1326</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">jj</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1327"></a><tt class="py-lineno">1327</tt>  <tt class="py-line">                <tt class="py-name">c2_yy</tt> <tt class="py-op">=</tt> <tt class="py-name">s_yy</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">ny</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1328"></a><tt class="py-lineno">1328</tt>  <tt class="py-line">                <tt class="py-name">beta1_yy</tt> <tt class="py-op">=</tt> <tt class="py-name">beta_cache_yy</tt><tt class="py-op">[</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1329"></a><tt class="py-lineno">1329</tt>  <tt class="py-line">                <tt class="py-name">beta2_yy</tt> <tt class="py-op">=</tt> <tt class="py-name">beta_cache_yy</tt><tt class="py-op">[</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">ny</tt><tt class="py-op">-</tt><tt class="py-name">jj</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1330"></a><tt class="py-lineno">1330</tt>  <tt class="py-line">                <tt class="py-name">over_y</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">c1_yy</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta1_yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta1_yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">c2_yy</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta2_yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta2_yy</tt><tt class="py-op">[</tt><tt class="py-name">nuax</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1331"></a><tt class="py-lineno">1331</tt>  <tt class="py-line">         </tt>
<a name="L1332"></a><tt class="py-lineno">1332</tt>  <tt class="py-line">                <tt class="py-name">s_xx</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">over_y</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">over_y</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1333"></a><tt class="py-lineno">1333</tt>  <tt class="py-line">                <tt class="py-name">c1_xx</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">over_y</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">s_xx</tt><tt class="py-op">*</tt><tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1334"></a><tt class="py-lineno">1334</tt>  <tt class="py-line">                <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1335"></a><tt class="py-lineno">1335</tt>  <tt class="py-line">                    <tt class="py-name">c2_xx</tt> <tt class="py-op">=</tt> <tt class="py-name">s_xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">nx</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1336"></a><tt class="py-lineno">1336</tt>  <tt class="py-line">                    <tt class="py-name">beta1_xx</tt> <tt class="py-op">=</tt> <tt class="py-name">beta_cache_xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1337"></a><tt class="py-lineno">1337</tt>  <tt class="py-line">                    <tt class="py-name">beta2_xx</tt> <tt class="py-op">=</tt> <tt class="py-name">beta_cache_xx</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">nx</tt><tt class="py-op">-</tt><tt class="py-name">ii</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1338"></a><tt class="py-lineno">1338</tt>  <tt class="py-line">                    <tt class="py-name">value</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">c1_xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta1_xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta1_xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">c2_xx</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">beta2_xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">beta2_xx</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1339"></a><tt class="py-lineno">1339</tt>  <tt class="py-line">                    <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">,</tt><tt class="py-name">jj</tt><tt class="py-op">,</tt><tt class="py-name">kk</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
<a name="L1340"></a><tt class="py-lineno">1340</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-132" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-132', 'dadi', 'link-2');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-133', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-134" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-134', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-135" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-135', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1341"></a><tt class="py-lineno">1341</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L1342"></a><tt class="py-lineno">1342</tt>  <tt class="py-line"> </tt>
<a name="L1343"></a><tt class="py-lineno">1343</tt>  <tt class="py-line"> </tt>
<a name="L1344"></a><tt class="py-lineno">1344</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum.from_phi"></a><div id="Spectrum.from_phi-def"><a name="L1345"></a><tt class="py-lineno">1345</tt> <a class="py-toggle" href="#" id="Spectrum.from_phi-toggle" onclick="return toggle('Spectrum.from_phi');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#from_phi">from_phi</a><tt class="py-op">(</tt><tt class="py-param">phi</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">xxs</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L1346"></a><tt class="py-lineno">1346</tt>  <tt class="py-line">                 <tt class="py-param">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">admix_props</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">het_ascertained</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt>  </tt>
<a name="L1347"></a><tt class="py-lineno">1347</tt>  <tt class="py-line">                 <tt class="py-param">force_direct</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.from_phi-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.from_phi-expanded"><a name="L1348"></a><tt class="py-lineno">1348</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1349"></a><tt class="py-lineno">1349</tt>  <tt class="py-line"><tt class="py-docstring">        Compute sample Spectrum from population frequency distribution phi.</tt> </tt>
<a name="L1350"></a><tt class="py-lineno">1350</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1351"></a><tt class="py-lineno">1351</tt>  <tt class="py-line"><tt class="py-docstring">        phi: P-dimensional population frequency distribution.</tt> </tt>
<a name="L1352"></a><tt class="py-lineno">1352</tt>  <tt class="py-line"><tt class="py-docstring">        ns: Sequence of P sample sizes for each population.</tt> </tt>
<a name="L1353"></a><tt class="py-lineno">1353</tt>  <tt class="py-line"><tt class="py-docstring">        xxs: Sequence of P one-dimesional grids on which phi is defined.</tt> </tt>
<a name="L1354"></a><tt class="py-lineno">1354</tt>  <tt class="py-line"><tt class="py-docstring">        mask_corners: If True, resulting FS is masked in 'absent' and 'fixed'</tt> </tt>
<a name="L1355"></a><tt class="py-lineno">1355</tt>  <tt class="py-line"><tt class="py-docstring">                      entries.</tt> </tt>
<a name="L1356"></a><tt class="py-lineno">1356</tt>  <tt class="py-line"><tt class="py-docstring">        pop_ids: Optional list of strings containing the population labels.</tt> </tt>
<a name="L1357"></a><tt class="py-lineno">1357</tt>  <tt class="py-line"><tt class="py-docstring">                 If pop_ids is None, labels will be "pop0", "pop1", ...</tt> </tt>
<a name="L1358"></a><tt class="py-lineno">1358</tt>  <tt class="py-line"><tt class="py-docstring">        admix_props: Admixture proportions for sampled individuals. For example,</tt> </tt>
<a name="L1359"></a><tt class="py-lineno">1359</tt>  <tt class="py-line"><tt class="py-docstring">                     if there are two populations, and individuals from the</tt> </tt>
<a name="L1360"></a><tt class="py-lineno">1360</tt>  <tt class="py-line"><tt class="py-docstring">                     first pop are admixed with fraction f from the second</tt> </tt>
<a name="L1361"></a><tt class="py-lineno">1361</tt>  <tt class="py-line"><tt class="py-docstring">                     population, then admix_props=((1-f,f),(0,1)). For three</tt> </tt>
<a name="L1362"></a><tt class="py-lineno">1362</tt>  <tt class="py-line"><tt class="py-docstring">                     populations, the no-admixture setting is</tt> </tt>
<a name="L1363"></a><tt class="py-lineno">1363</tt>  <tt class="py-line"><tt class="py-docstring">                     admix_props=((1,0,0),(0,1,0),(0,0,1)). </tt> </tt>
<a name="L1364"></a><tt class="py-lineno">1364</tt>  <tt class="py-line"><tt class="py-docstring">                     (Note that this option also forces direct integration,</tt> </tt>
<a name="L1365"></a><tt class="py-lineno">1365</tt>  <tt class="py-line"><tt class="py-docstring">                     which may be less accurate than the semi-analytic</tt> </tt>
<a name="L1366"></a><tt class="py-lineno">1366</tt>  <tt class="py-line"><tt class="py-docstring">                     method.)</tt> </tt>
<a name="L1367"></a><tt class="py-lineno">1367</tt>  <tt class="py-line"><tt class="py-docstring">        het_ascertained: If 'xx', then FS is calculated assuming that SNPs have</tt> </tt>
<a name="L1368"></a><tt class="py-lineno">1368</tt>  <tt class="py-line"><tt class="py-docstring">                         been ascertained by being heterozygous in one</tt> </tt>
<a name="L1369"></a><tt class="py-lineno">1369</tt>  <tt class="py-line"><tt class="py-docstring">                         individual from population 1. (This individual is</tt> </tt>
<a name="L1370"></a><tt class="py-lineno">1370</tt>  <tt class="py-line"><tt class="py-docstring">                         *not* in the current sample.) If 'yy' or 'zz', it</tt> </tt>
<a name="L1371"></a><tt class="py-lineno">1371</tt>  <tt class="py-line"><tt class="py-docstring">                         assumed that the ascertainment individual came from</tt> </tt>
<a name="L1372"></a><tt class="py-lineno">1372</tt>  <tt class="py-line"><tt class="py-docstring">                         population 2 or 3, respectively.</tt> </tt>
<a name="L1373"></a><tt class="py-lineno">1373</tt>  <tt class="py-line"><tt class="py-docstring">                         (Note that this option also forces direct integration,</tt> </tt>
<a name="L1374"></a><tt class="py-lineno">1374</tt>  <tt class="py-line"><tt class="py-docstring">                         which may be less accurate than the semi-analytic</tt> </tt>
<a name="L1375"></a><tt class="py-lineno">1375</tt>  <tt class="py-line"><tt class="py-docstring">                         method. This could be fixed if there is interest. Note</tt> </tt>
<a name="L1376"></a><tt class="py-lineno">1376</tt>  <tt class="py-line"><tt class="py-docstring">                         also that this option cannot be used simultaneously</tt> </tt>
<a name="L1377"></a><tt class="py-lineno">1377</tt>  <tt class="py-line"><tt class="py-docstring">                         with admix_props.)</tt> </tt>
<a name="L1378"></a><tt class="py-lineno">1378</tt>  <tt class="py-line"><tt class="py-docstring">        force_direct: Forces integration to use older direct integration method,</tt> </tt>
<a name="L1379"></a><tt class="py-lineno">1379</tt>  <tt class="py-line"><tt class="py-docstring">                      rather than using analytic integration of sampling </tt> </tt>
<a name="L1380"></a><tt class="py-lineno">1380</tt>  <tt class="py-line"><tt class="py-docstring">                      formula.</tt> </tt>
<a name="L1381"></a><tt class="py-lineno">1381</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1382"></a><tt class="py-lineno">1382</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">admix_props</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">allclose</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">admix_props</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1383"></a><tt class="py-lineno">1383</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Admixture proportions {0} must sum to 1 for all '</tt> </tt>
<a name="L1384"></a><tt class="py-lineno">1384</tt>  <tt class="py-line">                             <tt class="py-string">'populations.'</tt> <tt class="py-op">.</tt><tt class="py-name">format</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">admix_props</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1385"></a><tt class="py-lineno">1385</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xxs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1386"></a><tt class="py-lineno">1386</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Dimensionality of phi and lengths of ns and xxs '</tt> </tt>
<a name="L1387"></a><tt class="py-lineno">1387</tt>  <tt class="py-line">                             <tt class="py-string">'do not all agree.'</tt><tt class="py-op">)</tt> </tt>
<a name="L1388"></a><tt class="py-lineno">1388</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">'xx'</tt><tt class="py-op">,</tt><tt class="py-string">'yy'</tt><tt class="py-op">,</tt><tt class="py-string">'zz'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1389"></a><tt class="py-lineno">1389</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"If used, het_ascertained must be 'xx', 'yy', or "</tt> </tt>
<a name="L1390"></a><tt class="py-lineno">1390</tt>  <tt class="py-line">                             <tt class="py-string">"'zz'."</tt><tt class="py-op">)</tt> </tt>
<a name="L1391"></a><tt class="py-lineno">1391</tt>  <tt class="py-line"> </tt>
<a name="L1392"></a><tt class="py-lineno">1392</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">admix_props</tt> <tt class="py-keyword">and</tt> <tt class="py-name">het_ascertained</tt><tt class="py-op">:</tt> </tt>
<a name="L1393"></a><tt class="py-lineno">1393</tt>  <tt class="py-line">            <tt class="py-name">error</tt> <tt class="py-op">=</tt> <tt class="py-string">"""admix_props and het_ascertained options cannot be used </tt> </tt>
<a name="L1394"></a><tt class="py-lineno">1394</tt>  <tt class="py-line"><tt class="py-string">            simultaneously. Instead, please use the PhiManip methods to </tt> </tt>
<a name="L1395"></a><tt class="py-lineno">1395</tt>  <tt class="py-line"><tt class="py-string">            implement admixture. If this proves inappropriate for your use, </tt> </tt>
<a name="L1396"></a><tt class="py-lineno">1396</tt>  <tt class="py-line"><tt class="py-string">            contact the the dadi developers, as it may be possible to support</tt> </tt>
<a name="L1397"></a><tt class="py-lineno">1397</tt>  <tt class="py-line"><tt class="py-string">            both options simultaneously in the future."""</tt> </tt>
<a name="L1398"></a><tt class="py-lineno">1398</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-name">error</tt><tt class="py-op">)</tt> </tt>
<a name="L1399"></a><tt class="py-lineno">1399</tt>  <tt class="py-line"> </tt>
<a name="L1400"></a><tt class="py-lineno">1400</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L1401"></a><tt class="py-lineno">1401</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">force_direct</tt><tt class="py-op">:</tt> </tt>
<a name="L1402"></a><tt class="py-lineno">1402</tt>  <tt class="py-line">                <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-136" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-136', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-137" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum._from_phi_1D_analytic()=dadi.Spectrum_mod.Spectrum-class.html#_from_phi_1D_analytic"><a title="dadi.Spectrum_mod.Spectrum._from_phi_1D_analytic" class="py-name" href="#" onclick="return doclink('link-137', '_from_phi_1D_analytic', 'link-137');">_from_phi_1D_analytic</a></tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt> </tt>
<a name="L1403"></a><tt class="py-lineno">1403</tt>  <tt class="py-line">                                                    <tt id="link-138" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-138', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1404"></a><tt class="py-lineno">1404</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1405"></a><tt class="py-lineno">1405</tt>  <tt class="py-line">                <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-139" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-139', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-140" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum._from_phi_1D_direct()=dadi.Spectrum_mod.Spectrum-class.html#_from_phi_1D_direct"><a title="dadi.Spectrum_mod.Spectrum._from_phi_1D_direct" class="py-name" href="#" onclick="return doclink('link-140', '_from_phi_1D_direct', 'link-140');">_from_phi_1D_direct</a></tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt>  </tt>
<a name="L1406"></a><tt class="py-lineno">1406</tt>  <tt class="py-line">                                                  <tt id="link-141" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-141', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt> <tt class="py-name">het_ascertained</tt><tt class="py-op">)</tt> </tt>
<a name="L1407"></a><tt class="py-lineno">1407</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L1408"></a><tt class="py-lineno">1408</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">admix_props</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">force_direct</tt><tt class="py-op">:</tt> </tt>
<a name="L1409"></a><tt class="py-lineno">1409</tt>  <tt class="py-line">                <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-142" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-142', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-143" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum._from_phi_2D_analytic()=dadi.Spectrum_mod.Spectrum-class.html#_from_phi_2D_analytic"><a title="dadi.Spectrum_mod.Spectrum._from_phi_2D_analytic" class="py-name" href="#" onclick="return doclink('link-143', '_from_phi_2D_analytic', 'link-143');">_from_phi_2D_analytic</a></tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1410"></a><tt class="py-lineno">1410</tt>  <tt class="py-line">                                                    <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">,</tt> </tt>
<a name="L1411"></a><tt class="py-lineno">1411</tt>  <tt class="py-line">                                                    <tt id="link-144" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-144', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1412"></a><tt class="py-lineno">1412</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">admix_props</tt><tt class="py-op">:</tt> </tt>
<a name="L1413"></a><tt class="py-lineno">1413</tt>  <tt class="py-line">                <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-145" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-145', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-146" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum._from_phi_2D_direct()=dadi.Spectrum_mod.Spectrum-class.html#_from_phi_2D_direct"><a title="dadi.Spectrum_mod.Spectrum._from_phi_2D_direct" class="py-name" href="#" onclick="return doclink('link-146', '_from_phi_2D_direct', 'link-146');">_from_phi_2D_direct</a></tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1414"></a><tt class="py-lineno">1414</tt>  <tt class="py-line">                                                  <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt id="link-147" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-147', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt>  </tt>
<a name="L1415"></a><tt class="py-lineno">1415</tt>  <tt class="py-line">                                                  <tt class="py-name">het_ascertained</tt><tt class="py-op">)</tt> </tt>
<a name="L1416"></a><tt class="py-lineno">1416</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1417"></a><tt class="py-lineno">1417</tt>  <tt class="py-line">                <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-148" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-148', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt class="py-name">from_phi_2D_admix_props</tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1418"></a><tt class="py-lineno">1418</tt>  <tt class="py-line">                                                      <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1419"></a><tt class="py-lineno">1419</tt>  <tt class="py-line">                                                      <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt id="link-149" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-149', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt>  </tt>
<a name="L1420"></a><tt class="py-lineno">1420</tt>  <tt class="py-line">                                                      <tt class="py-name">admix_props</tt><tt class="py-op">)</tt> </tt>
<a name="L1421"></a><tt class="py-lineno">1421</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">phi</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L1422"></a><tt class="py-lineno">1422</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">het_ascertained</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">admix_props</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">force_direct</tt><tt class="py-op">:</tt> </tt>
<a name="L1423"></a><tt class="py-lineno">1423</tt>  <tt class="py-line">                <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-150" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-150', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-151" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum._from_phi_3D_analytic()=dadi.Spectrum_mod.Spectrum-class.html#_from_phi_3D_analytic"><a title="dadi.Spectrum_mod.Spectrum._from_phi_3D_analytic" class="py-name" href="#" onclick="return doclink('link-151', '_from_phi_3D_analytic', 'link-151');">_from_phi_3D_analytic</a></tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1424"></a><tt class="py-lineno">1424</tt>  <tt class="py-line">                                                    <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1425"></a><tt class="py-lineno">1425</tt>  <tt class="py-line">                                                    <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt id="link-152" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-152', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1426"></a><tt class="py-lineno">1426</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">admix_props</tt><tt class="py-op">:</tt> </tt>
<a name="L1427"></a><tt class="py-lineno">1427</tt>  <tt class="py-line">                <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-153" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-153', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-154" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum._from_phi_3D_direct()=dadi.Spectrum_mod.Spectrum-class.html#_from_phi_3D_direct"><a title="dadi.Spectrum_mod.Spectrum._from_phi_3D_direct" class="py-name" href="#" onclick="return doclink('link-154', '_from_phi_3D_direct', 'link-154');">_from_phi_3D_direct</a></tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1428"></a><tt class="py-lineno">1428</tt>  <tt class="py-line">                                                  <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1429"></a><tt class="py-lineno">1429</tt>  <tt class="py-line">                                                  <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt id="link-155" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-155', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt>  </tt>
<a name="L1430"></a><tt class="py-lineno">1430</tt>  <tt class="py-line">                                                  <tt class="py-name">het_ascertained</tt><tt class="py-op">)</tt> </tt>
<a name="L1431"></a><tt class="py-lineno">1431</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1432"></a><tt class="py-lineno">1432</tt>  <tt class="py-line">                <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-156" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-156', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-157" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum._from_phi_3D_admix_props()=dadi.Spectrum_mod.Spectrum-class.html#_from_phi_3D_admix_props"><a title="dadi.Spectrum_mod.Spectrum._from_phi_3D_admix_props" class="py-name" href="#" onclick="return doclink('link-157', '_from_phi_3D_admix_props', 'link-157');">_from_phi_3D_admix_props</a></tt><tt class="py-op">(</tt><tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1433"></a><tt class="py-lineno">1433</tt>  <tt class="py-line">                                                       <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt>  </tt>
<a name="L1434"></a><tt class="py-lineno">1434</tt>  <tt class="py-line">                                                       <tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt id="link-158" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-158', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt>  </tt>
<a name="L1435"></a><tt class="py-lineno">1435</tt>  <tt class="py-line">                                                       <tt class="py-name">admix_props</tt><tt class="py-op">)</tt> </tt>
<a name="L1436"></a><tt class="py-lineno">1436</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1437"></a><tt class="py-lineno">1437</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Only implemented for dimensions 1,2 or 3.'</tt><tt class="py-op">)</tt> </tt>
<a name="L1438"></a><tt class="py-lineno">1438</tt>  <tt class="py-line">        <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt> <tt class="py-op">=</tt> <tt class="py-name">pop_ids</tt> </tt>
<a name="L1439"></a><tt class="py-lineno">1439</tt>  <tt class="py-line">        <tt class="py-comment"># Record value to use for extrapolation. This is the first grid point,</tt> </tt>
<a name="L1440"></a><tt class="py-lineno">1440</tt>  <tt class="py-line">        <tt class="py-comment"># which is where new mutations are introduced. Note that extrapolation</tt> </tt>
<a name="L1441"></a><tt class="py-lineno">1441</tt>  <tt class="py-line">        <tt class="py-comment"># will likely fail if grids differ between dimensions.</tt> </tt>
<a name="L1442"></a><tt class="py-lineno">1442</tt>  <tt class="py-line">        <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt> <tt class="py-op">=</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1443"></a><tt class="py-lineno">1443</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">xx</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xxs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1444"></a><tt class="py-lineno">1444</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">xx</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt><tt class="py-op">:</tt> </tt>
<a name="L1445"></a><tt class="py-lineno">1445</tt>  <tt class="py-line">                <tt id="link-159" class="py-name"><a title="dadi.Hessian.logger
dadi.Inference.logger
dadi.Integration.logger
dadi.Numerics.logger
dadi.RunInParallel.logger
dadi.Spectrum_mod.logger" class="py-name" href="#" onclick="return doclink('link-159', 'logger', 'link-0');">logger</a></tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">'Spectrum calculated from phi different grids for '</tt> </tt>
<a name="L1446"></a><tt class="py-lineno">1446</tt>  <tt class="py-line">                            <tt class="py-string">'different dimensions. Extrapolation may fail.'</tt><tt class="py-op">)</tt> </tt>
<a name="L1447"></a><tt class="py-lineno">1447</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L1448"></a><tt class="py-lineno">1448</tt>  <tt class="py-line"> </tt>
<a name="Spectrum.scramble_pop_ids"></a><div id="Spectrum.scramble_pop_ids-def"><a name="L1449"></a><tt class="py-lineno">1449</tt> <a class="py-toggle" href="#" id="Spectrum.scramble_pop_ids-toggle" onclick="return toggle('Spectrum.scramble_pop_ids');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#scramble_pop_ids">scramble_pop_ids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.scramble_pop_ids-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.scramble_pop_ids-expanded"><a name="L1450"></a><tt class="py-lineno">1450</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1451"></a><tt class="py-lineno">1451</tt>  <tt class="py-line"><tt class="py-docstring">        Spectrum corresponding to scrambling individuals among populations.</tt> </tt>
<a name="L1452"></a><tt class="py-lineno">1452</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L1453"></a><tt class="py-lineno">1453</tt>  <tt class="py-line"><tt class="py-docstring">        This is useful for assessing how diverged populations are.</tt> </tt>
<a name="L1454"></a><tt class="py-lineno">1454</tt>  <tt class="py-line"><tt class="py-docstring">        Essentially, it pools all the individuals represented in the fs and</tt> </tt>
<a name="L1455"></a><tt class="py-lineno">1455</tt>  <tt class="py-line"><tt class="py-docstring">        generates new populations of random individuals (without replacement)</tt> </tt>
<a name="L1456"></a><tt class="py-lineno">1456</tt>  <tt class="py-line"><tt class="py-docstring">        from that pool. If this fs is significantly different from the</tt> </tt>
<a name="L1457"></a><tt class="py-lineno">1457</tt>  <tt class="py-line"><tt class="py-docstring">        original, that implies population structure.</tt> </tt>
<a name="L1458"></a><tt class="py-lineno">1458</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1459"></a><tt class="py-lineno">1459</tt>  <tt class="py-line">        <tt class="py-name">original_folded</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> </tt>
<a name="L1460"></a><tt class="py-lineno">1460</tt>  <tt class="py-line">        <tt class="py-comment"># If we started with an folded Spectrum, we need to unfold before</tt> </tt>
<a name="L1461"></a><tt class="py-lineno">1461</tt>  <tt class="py-line">        <tt class="py-comment"># projecting.</tt> </tt>
<a name="L1462"></a><tt class="py-lineno">1462</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">original_folded</tt><tt class="py-op">:</tt> </tt>
<a name="L1463"></a><tt class="py-lineno">1463</tt>  <tt class="py-line">            <tt class="py-name">self</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.unfold" class="py-name" href="#" onclick="return doclink('link-160', 'unfold', 'link-35');">unfold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1464"></a><tt class="py-lineno">1464</tt>  <tt class="py-line"> </tt>
<a name="L1465"></a><tt class="py-lineno">1465</tt>  <tt class="py-line">        <tt class="py-name">total_samp</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-161', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1466"></a><tt class="py-lineno">1466</tt>  <tt class="py-line">     </tt>
<a name="L1467"></a><tt class="py-lineno">1467</tt>  <tt class="py-line">        <tt class="py-comment"># First generate a 1d sfs for the pooled population.</tt> </tt>
<a name="L1468"></a><tt class="py-lineno">1468</tt>  <tt class="py-line">        <tt class="py-name">combined</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">total_samp</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1469"></a><tt class="py-lineno">1469</tt>  <tt class="py-line">        <tt class="py-comment"># For each entry in the fs, this is the total number of derived alleles</tt> </tt>
<a name="L1470"></a><tt class="py-lineno">1470</tt>  <tt class="py-line">        <tt class="py-name">total_per_entry</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="dadi.Spectrum_mod.Spectrum._total_per_entry" class="py-name" href="#" onclick="return doclink('link-162', '_total_per_entry', 'link-10');">_total_per_entry</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1471"></a><tt class="py-lineno">1471</tt>  <tt class="py-line">        <tt class="py-comment"># Sum up to generate the equivalent 1-d spectrum.</tt> </tt>
<a name="L1472"></a><tt class="py-lineno">1472</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">derived</tt><tt class="py-op">,</tt><tt class="py-name">counts</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">total_per_entry</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1473"></a><tt class="py-lineno">1473</tt>  <tt class="py-line">            <tt class="py-name">combined</tt><tt class="py-op">[</tt><tt class="py-name">derived</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">counts</tt> </tt>
<a name="L1474"></a><tt class="py-lineno">1474</tt>  <tt class="py-line">     </tt>
<a name="L1475"></a><tt class="py-lineno">1475</tt>  <tt class="py-line">        <tt class="py-comment"># Now resample back into a n-d spectrum</tt> </tt>
<a name="L1476"></a><tt class="py-lineno">1476</tt>  <tt class="py-line">        <tt class="py-comment"># For each entry, this is the counts per popuation. </tt> </tt>
<a name="L1477"></a><tt class="py-lineno">1477</tt>  <tt class="py-line">        <tt class="py-comment">#  e.g. counts_per_entry[3,4,5] = [3,4,5]</tt> </tt>
<a name="L1478"></a><tt class="py-lineno">1478</tt>  <tt class="py-line">        <tt class="py-name">counts_per_entry</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="dadi.Spectrum_mod.Spectrum._counts_per_entry" class="py-name" href="#" onclick="return doclink('link-163', '_counts_per_entry', 'link-54');">_counts_per_entry</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1479"></a><tt class="py-lineno">1479</tt>  <tt class="py-line">        <tt class="py-comment"># Reshape it to be 1-d, so we can iterate over it easily.</tt> </tt>
<a name="L1480"></a><tt class="py-lineno">1480</tt>  <tt class="py-line">        <tt class="py-name">counts_per_entry</tt> <tt class="py-op">=</tt> <tt class="py-name">counts_per_entry</tt><tt class="py-op">.</tt><tt class="py-name">reshape</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">prod</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>  </tt>
<a name="L1481"></a><tt class="py-lineno">1481</tt>  <tt class="py-line">                                                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ndim</tt><tt class="py-op">)</tt> </tt>
<a name="L1482"></a><tt class="py-lineno">1482</tt>  <tt class="py-line">        <tt class="py-name">resamp</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L1483"></a><tt class="py-lineno">1483</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">counts</tt><tt class="py-op">,</tt> <tt class="py-name">derived</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">counts_per_entry</tt><tt class="py-op">,</tt> <tt class="py-name">total_per_entry</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1484"></a><tt class="py-lineno">1484</tt>  <tt class="py-line">            <tt class="py-comment"># The probability here is </tt> </tt>
<a name="L1485"></a><tt class="py-lineno">1485</tt>  <tt class="py-line">            <tt class="py-comment"># (t1 choose d1)*(t2 choose d2)/(ntot choose derived)</tt> </tt>
<a name="L1486"></a><tt class="py-lineno">1486</tt>  <tt class="py-line">            <tt class="py-name">lnprob</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt id="link-164" class="py-name"><a title="dadi.Numerics._lncomb" class="py-name" href="#" onclick="return doclink('link-164', '_lncomb', 'link-8');">_lncomb</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt><tt class="py-op">,</tt><tt class="py-name">d</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.sample_sizes" class="py-name" href="#" onclick="return doclink('link-165', 'sample_sizes', 'link-9');">sample_sizes</a></tt><tt class="py-op">,</tt><tt class="py-name">counts</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1487"></a><tt class="py-lineno">1487</tt>  <tt class="py-line">            <tt class="py-name">lnprob</tt> <tt class="py-op">-=</tt> <tt id="link-166" class="py-name"><a title="dadi.Numerics._lncomb" class="py-name" href="#" onclick="return doclink('link-166', '_lncomb', 'link-8');">_lncomb</a></tt><tt class="py-op">(</tt><tt class="py-name">total_samp</tt><tt class="py-op">,</tt> <tt class="py-name">derived</tt><tt class="py-op">)</tt> </tt>
<a name="L1488"></a><tt class="py-lineno">1488</tt>  <tt class="py-line">            <tt class="py-name">prob</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-name">lnprob</tt><tt class="py-op">)</tt> </tt>
<a name="L1489"></a><tt class="py-lineno">1489</tt>  <tt class="py-line">            <tt class="py-comment"># Assign result using the appropriate weighting</tt> </tt>
<a name="L1490"></a><tt class="py-lineno">1490</tt>  <tt class="py-line">            <tt class="py-name">resamp</tt><tt class="py-op">[</tt><tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">counts</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">prob</tt><tt class="py-op">*</tt><tt class="py-name">combined</tt><tt class="py-op">[</tt><tt class="py-name">derived</tt><tt class="py-op">]</tt> </tt>
<a name="L1491"></a><tt class="py-lineno">1491</tt>  <tt class="py-line"> </tt>
<a name="L1492"></a><tt class="py-lineno">1492</tt>  <tt class="py-line">        <tt class="py-name">resamp</tt> <tt class="py-op">=</tt> <tt id="link-167" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-167', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">resamp</tt><tt class="py-op">,</tt> <tt id="link-168" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-168', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-169" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-169', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">)</tt> </tt>
<a name="L1493"></a><tt class="py-lineno">1493</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">original_folded</tt><tt class="py-op">:</tt> </tt>
<a name="L1494"></a><tt class="py-lineno">1494</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">resamp</tt> </tt>
<a name="L1495"></a><tt class="py-lineno">1495</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1496"></a><tt class="py-lineno">1496</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">resamp</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.fold" class="py-name" href="#" onclick="return doclink('link-170', 'fold', 'link-38');">fold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1497"></a><tt class="py-lineno">1497</tt>  <tt class="py-line"> </tt>
<a name="L1498"></a><tt class="py-lineno">1498</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum.from_data_dict"></a><div id="Spectrum.from_data_dict-def"><a name="L1499"></a><tt class="py-lineno">1499</tt> <a class="py-toggle" href="#" id="Spectrum.from_data_dict-toggle" onclick="return toggle('Spectrum.from_data_dict');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#from_data_dict">from_data_dict</a><tt class="py-op">(</tt><tt class="py-param">data_dict</tt><tt class="py-op">,</tt> <tt class="py-param">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-param">projections</tt><tt class="py-op">,</tt> <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> </tt>
<a name="L1500"></a><tt class="py-lineno">1500</tt>  <tt class="py-line">                       <tt class="py-param">polarized</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.from_data_dict-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.from_data_dict-expanded"><a name="L1501"></a><tt class="py-lineno">1501</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1502"></a><tt class="py-lineno">1502</tt>  <tt class="py-line"><tt class="py-docstring">        Spectrum from a dictionary of polymorphisms.</tt> </tt>
<a name="L1503"></a><tt class="py-lineno">1503</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1504"></a><tt class="py-lineno">1504</tt>  <tt class="py-line"><tt class="py-docstring">        pop_ids: list of which populations to make fs for.</tt> </tt>
<a name="L1505"></a><tt class="py-lineno">1505</tt>  <tt class="py-line"><tt class="py-docstring">        projections: list of sample sizes to project down to for each</tt> </tt>
<a name="L1506"></a><tt class="py-lineno">1506</tt>  <tt class="py-line"><tt class="py-docstring">                     population.</tt> </tt>
<a name="L1507"></a><tt class="py-lineno">1507</tt>  <tt class="py-line"><tt class="py-docstring">        polarized: If True, the data are assumed to be correctly polarized by </tt> </tt>
<a name="L1508"></a><tt class="py-lineno">1508</tt>  <tt class="py-line"><tt class="py-docstring">                   `outgroup_allele'. SNPs in which the 'outgroup_allele'</tt> </tt>
<a name="L1509"></a><tt class="py-lineno">1509</tt>  <tt class="py-line"><tt class="py-docstring">                   information is missing or '-' or not concordant with the</tt> </tt>
<a name="L1510"></a><tt class="py-lineno">1510</tt>  <tt class="py-line"><tt class="py-docstring">                   segregating alleles will be ignored.</tt> </tt>
<a name="L1511"></a><tt class="py-lineno">1511</tt>  <tt class="py-line"><tt class="py-docstring">                   If False, any 'outgroup_allele' info present is ignored,</tt> </tt>
<a name="L1512"></a><tt class="py-lineno">1512</tt>  <tt class="py-line"><tt class="py-docstring">                   and the returned spectrum is folded.</tt> </tt>
<a name="L1513"></a><tt class="py-lineno">1513</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1514"></a><tt class="py-lineno">1514</tt>  <tt class="py-line"><tt class="py-docstring">        The data dictionary should be organized as:</tt> </tt>
<a name="L1515"></a><tt class="py-lineno">1515</tt>  <tt class="py-line"><tt class="py-docstring">            {snp_id:{'segregating': ['A','T'],</tt> </tt>
<a name="L1516"></a><tt class="py-lineno">1516</tt>  <tt class="py-line"><tt class="py-docstring">                     'calls': {'YRI': (23,3),</tt> </tt>
<a name="L1517"></a><tt class="py-lineno">1517</tt>  <tt class="py-line"><tt class="py-docstring">                                'CEU': (7,3)</tt> </tt>
<a name="L1518"></a><tt class="py-lineno">1518</tt>  <tt class="py-line"><tt class="py-docstring">                                },</tt> </tt>
<a name="L1519"></a><tt class="py-lineno">1519</tt>  <tt class="py-line"><tt class="py-docstring">                     'outgroup_allele': 'T'</tt> </tt>
<a name="L1520"></a><tt class="py-lineno">1520</tt>  <tt class="py-line"><tt class="py-docstring">                    }</tt> </tt>
<a name="L1521"></a><tt class="py-lineno">1521</tt>  <tt class="py-line"><tt class="py-docstring">            }</tt> </tt>
<a name="L1522"></a><tt class="py-lineno">1522</tt>  <tt class="py-line"><tt class="py-docstring">        The 'calls' entry gives the successful calls in each population, in the</tt> </tt>
<a name="L1523"></a><tt class="py-lineno">1523</tt>  <tt class="py-line"><tt class="py-docstring">        order that the alleles are specified in 'segregating'.</tt> </tt>
<a name="L1524"></a><tt class="py-lineno">1524</tt>  <tt class="py-line"><tt class="py-docstring">        Non-diallelic polymorphisms are skipped.</tt> </tt>
<a name="L1525"></a><tt class="py-lineno">1525</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1526"></a><tt class="py-lineno">1526</tt>  <tt class="py-line">        <tt class="py-name">Npops</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L1527"></a><tt class="py-lineno">1527</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">projections</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1528"></a><tt class="py-lineno">1528</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">snp</tt><tt class="py-op">,</tt> <tt class="py-name">snp_info</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data_dict</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1529"></a><tt class="py-lineno">1529</tt>  <tt class="py-line">            <tt class="py-comment"># Skip SNPs that aren't triallelic.</tt> </tt>
<a name="L1530"></a><tt class="py-lineno">1530</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'segregating'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L1531"></a><tt class="py-lineno">1531</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L1532"></a><tt class="py-lineno">1532</tt>  <tt class="py-line"> </tt>
<a name="L1533"></a><tt class="py-lineno">1533</tt>  <tt class="py-line">            <tt class="py-name">allele1</tt><tt class="py-op">,</tt><tt class="py-name">allele2</tt> <tt class="py-op">=</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'segregating'</tt><tt class="py-op">]</tt> </tt>
<a name="L1534"></a><tt class="py-lineno">1534</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">polarized</tt><tt class="py-op">:</tt> </tt>
<a name="L1535"></a><tt class="py-lineno">1535</tt>  <tt class="py-line">                <tt class="py-comment"># If we don't want to polarize, we can choose which allele is</tt> </tt>
<a name="L1536"></a><tt class="py-lineno">1536</tt>  <tt class="py-line">                <tt class="py-comment"># derived arbitrarily since we'll fold anyways.</tt> </tt>
<a name="L1537"></a><tt class="py-lineno">1537</tt>  <tt class="py-line">                <tt class="py-name">outgroup_allele</tt> <tt class="py-op">=</tt> <tt class="py-name">allele1</tt> </tt>
<a name="L1538"></a><tt class="py-lineno">1538</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-string">'outgroup_allele'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">snp_info</tt>\ </tt>
<a name="L1539"></a><tt class="py-lineno">1539</tt>  <tt class="py-line">               <tt class="py-keyword">and</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'outgroup_allele'</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">'-'</tt>\ </tt>
<a name="L1540"></a><tt class="py-lineno">1540</tt>  <tt class="py-line">               <tt class="py-keyword">and</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'outgroup_allele'</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'segregating'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1541"></a><tt class="py-lineno">1541</tt>  <tt class="py-line">                <tt class="py-comment"># Otherwise we need to check that it's a useful outgroup</tt> </tt>
<a name="L1542"></a><tt class="py-lineno">1542</tt>  <tt class="py-line">                <tt class="py-name">outgroup_allele</tt> <tt class="py-op">=</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'outgroup_allele'</tt><tt class="py-op">]</tt> </tt>
<a name="L1543"></a><tt class="py-lineno">1543</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt>  </tt>
<a name="L1544"></a><tt class="py-lineno">1544</tt>  <tt class="py-line">                <tt class="py-comment"># If we're polarized and we didn't have good outgroup info, skip</tt> </tt>
<a name="L1545"></a><tt class="py-lineno">1545</tt>  <tt class="py-line">                <tt class="py-comment"># this SNP.</tt> </tt>
<a name="L1546"></a><tt class="py-lineno">1546</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L1547"></a><tt class="py-lineno">1547</tt>  <tt class="py-line">     </tt>
<a name="L1548"></a><tt class="py-lineno">1548</tt>  <tt class="py-line">            <tt class="py-comment"># Extract the allele calls for each population.</tt> </tt>
<a name="L1549"></a><tt class="py-lineno">1549</tt>  <tt class="py-line">            <tt class="py-name">allele1_calls</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'calls'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">pop</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L1550"></a><tt class="py-lineno">1550</tt>  <tt class="py-line">                                            <tt class="py-keyword">for</tt> <tt class="py-name">pop</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1551"></a><tt class="py-lineno">1551</tt>  <tt class="py-line">            <tt class="py-name">allele2_calls</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'calls'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">pop</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1552"></a><tt class="py-lineno">1552</tt>  <tt class="py-line">                                            <tt class="py-keyword">for</tt> <tt class="py-name">pop</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1553"></a><tt class="py-lineno">1553</tt>  <tt class="py-line">            <tt class="py-comment"># How many chromosomes did we call successfully in each population?</tt> </tt>
<a name="L1554"></a><tt class="py-lineno">1554</tt>  <tt class="py-line">            <tt class="py-name">successful_calls</tt> <tt class="py-op">=</tt> <tt class="py-name">allele1_calls</tt> <tt class="py-op">+</tt> <tt class="py-name">allele2_calls</tt> </tt>
<a name="L1555"></a><tt class="py-lineno">1555</tt>  <tt class="py-line">     </tt>
<a name="L1556"></a><tt class="py-lineno">1556</tt>  <tt class="py-line">            <tt class="py-comment"># Which allele is derived (different from outgroup)?</tt> </tt>
<a name="L1557"></a><tt class="py-lineno">1557</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">allele1</tt> <tt class="py-op">==</tt> <tt class="py-name">outgroup_allele</tt><tt class="py-op">:</tt> </tt>
<a name="L1558"></a><tt class="py-lineno">1558</tt>  <tt class="py-line">                <tt class="py-name">derived_calls</tt> <tt class="py-op">=</tt> <tt class="py-name">allele2_calls</tt> </tt>
<a name="L1559"></a><tt class="py-lineno">1559</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">allele2</tt> <tt class="py-op">==</tt> <tt class="py-name">outgroup_allele</tt><tt class="py-op">:</tt> </tt>
<a name="L1560"></a><tt class="py-lineno">1560</tt>  <tt class="py-line">                <tt class="py-name">derived_calls</tt> <tt class="py-op">=</tt> <tt class="py-name">allele1_calls</tt> </tt>
<a name="L1561"></a><tt class="py-lineno">1561</tt>  <tt class="py-line">     </tt>
<a name="L1562"></a><tt class="py-lineno">1562</tt>  <tt class="py-line">            <tt class="py-comment"># To handle arbitrary numbers of populations in the fs, we need</tt> </tt>
<a name="L1563"></a><tt class="py-lineno">1563</tt>  <tt class="py-line">            <tt class="py-comment"># to do some tricky slicing.</tt> </tt>
<a name="L1564"></a><tt class="py-lineno">1564</tt>  <tt class="py-line">            <tt class="py-name">slices</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">newaxis</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">Npops</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L1565"></a><tt class="py-lineno">1565</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">ii</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1566"></a><tt class="py-lineno">1566</tt>  <tt class="py-line">                <tt class="py-name">slices</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">ii</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L1567"></a><tt class="py-lineno">1567</tt>  <tt class="py-line">         </tt>
<a name="L1568"></a><tt class="py-lineno">1568</tt>  <tt class="py-line">            <tt class="py-comment"># Do the projection for this SNP.</tt> </tt>
<a name="L1569"></a><tt class="py-lineno">1569</tt>  <tt class="py-line">            <tt class="py-name">pop_contribs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L1570"></a><tt class="py-lineno">1570</tt>  <tt class="py-line">            <tt class="py-name">iter</tt> <tt class="py-op">=</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">projections</tt><tt class="py-op">,</tt> <tt class="py-name">successful_calls</tt><tt class="py-op">,</tt> <tt class="py-name">derived_calls</tt><tt class="py-op">)</tt> </tt>
<a name="L1571"></a><tt class="py-lineno">1571</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt class="py-name">pop_ii</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">p_to</tt><tt class="py-op">,</tt> <tt class="py-name">p_from</tt><tt class="py-op">,</tt> <tt class="py-name">hits</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">iter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1572"></a><tt class="py-lineno">1572</tt>  <tt class="py-line">                <tt class="py-name">contrib</tt> <tt class="py-op">=</tt> <tt id="link-171" class="py-name"><a title="dadi.Numerics._cached_projection" class="py-name" href="#" onclick="return doclink('link-171', '_cached_projection', 'link-7');">_cached_projection</a></tt><tt class="py-op">(</tt><tt class="py-name">p_to</tt><tt class="py-op">,</tt><tt class="py-name">p_from</tt><tt class="py-op">,</tt><tt class="py-name">hits</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">slices</tt><tt class="py-op">[</tt><tt class="py-name">pop_ii</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L1573"></a><tt class="py-lineno">1573</tt>  <tt class="py-line">                <tt class="py-name">pop_contribs</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">contrib</tt><tt class="py-op">)</tt> </tt>
<a name="L1574"></a><tt class="py-lineno">1574</tt>  <tt class="py-line">            <tt class="py-name">fs</tt> <tt class="py-op">+=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-name">operator</tt><tt class="py-op">.</tt><tt class="py-name">mul</tt><tt class="py-op">,</tt> <tt class="py-name">pop_contribs</tt><tt class="py-op">)</tt> </tt>
<a name="L1575"></a><tt class="py-lineno">1575</tt>  <tt class="py-line">        <tt class="py-name">fsout</tt> <tt class="py-op">=</tt> <tt id="link-172" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-172', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">,</tt> <tt id="link-173" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-173', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-174" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-174', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt>  </tt>
<a name="L1576"></a><tt class="py-lineno">1576</tt>  <tt class="py-line">                         <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
<a name="L1577"></a><tt class="py-lineno">1577</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">polarized</tt><tt class="py-op">:</tt> </tt>
<a name="L1578"></a><tt class="py-lineno">1578</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fsout</tt> </tt>
<a name="L1579"></a><tt class="py-lineno">1579</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L1580"></a><tt class="py-lineno">1580</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">fsout</tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.fold" class="py-name" href="#" onclick="return doclink('link-175', 'fold', 'link-38');">fold</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1581"></a><tt class="py-lineno">1581</tt>  <tt class="py-line">     </tt>
<a name="L1582"></a><tt class="py-lineno">1582</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum._data_by_tri"></a><div id="Spectrum._data_by_tri-def"><a name="L1583"></a><tt class="py-lineno">1583</tt> <a class="py-toggle" href="#" id="Spectrum._data_by_tri-toggle" onclick="return toggle('Spectrum._data_by_tri');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_data_by_tri">_data_by_tri</a><tt class="py-op">(</tt><tt class="py-param">data_dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._data_by_tri-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._data_by_tri-expanded"><a name="L1584"></a><tt class="py-lineno">1584</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1585"></a><tt class="py-lineno">1585</tt>  <tt class="py-line"><tt class="py-docstring">        Nest the data by derived context and outgroup base.</tt> </tt>
<a name="L1586"></a><tt class="py-lineno">1586</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1587"></a><tt class="py-lineno">1587</tt>  <tt class="py-line"><tt class="py-docstring">        The resulting dictionary contains only SNPs which are appropriate for</tt> </tt>
<a name="L1588"></a><tt class="py-lineno">1588</tt>  <tt class="py-line"><tt class="py-docstring">        use of Hernandez's ancestral misidentification correction. It is</tt> </tt>
<a name="L1589"></a><tt class="py-lineno">1589</tt>  <tt class="py-line"><tt class="py-docstring">        organized as {(derived_tri, outgroup_base): {snp_id: data,...}}</tt> </tt>
<a name="L1590"></a><tt class="py-lineno">1590</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1591"></a><tt class="py-lineno">1591</tt>  <tt class="py-line">        <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1592"></a><tt class="py-lineno">1592</tt>  <tt class="py-line">        <tt class="py-name">genetic_bases</tt> <tt class="py-op">=</tt> <tt class="py-string">'ACTG'</tt> </tt>
<a name="L1593"></a><tt class="py-lineno">1593</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">snp</tt><tt class="py-op">,</tt> <tt class="py-name">snp_info</tt> <tt class="py-keyword">in</tt> <tt class="py-name">data_dict</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1594"></a><tt class="py-lineno">1594</tt>  <tt class="py-line">            <tt class="py-comment"># Skip non-diallelic polymorphisms</tt> </tt>
<a name="L1595"></a><tt class="py-lineno">1595</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'segregating'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L1596"></a><tt class="py-lineno">1596</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L1597"></a><tt class="py-lineno">1597</tt>  <tt class="py-line">            <tt class="py-name">allele1</tt><tt class="py-op">,</tt> <tt class="py-name">allele2</tt> <tt class="py-op">=</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'segregating'</tt><tt class="py-op">]</tt> </tt>
<a name="L1598"></a><tt class="py-lineno">1598</tt>  <tt class="py-line">            <tt class="py-comment"># Filter out SNPs where we either non-constant ingroup or outgroup</tt> </tt>
<a name="L1599"></a><tt class="py-lineno">1599</tt>  <tt class="py-line">            <tt class="py-comment"># context.</tt> </tt>
<a name="L1600"></a><tt class="py-lineno">1600</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L1601"></a><tt class="py-lineno">1601</tt>  <tt class="py-line">                <tt class="py-name">ingroup_tri</tt> <tt class="py-op">=</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'context'</tt><tt class="py-op">]</tt> </tt>
<a name="L1602"></a><tt class="py-lineno">1602</tt>  <tt class="py-line">                <tt class="py-name">outgroup_tri</tt> <tt class="py-op">=</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'outgroup_context'</tt><tt class="py-op">]</tt> </tt>
<a name="L1603"></a><tt class="py-lineno">1603</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L1604"></a><tt class="py-lineno">1604</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L1605"></a><tt class="py-lineno">1605</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">outgroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">snp_info</tt><tt class="py-op">[</tt><tt class="py-string">'outgroup_allele'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1606"></a><tt class="py-lineno">1606</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Outgroup context and allele are inconsistent '</tt> </tt>
<a name="L1607"></a><tt class="py-lineno">1607</tt>  <tt class="py-line">                                 <tt class="py-string">'for polymorphism: %s.'</tt> <tt class="py-op">%</tt> <tt class="py-name">snp</tt><tt class="py-op">)</tt> </tt>
<a name="L1608"></a><tt class="py-lineno">1608</tt>  <tt class="py-line">            <tt class="py-name">outgroup_allele</tt> <tt class="py-op">=</tt> <tt class="py-name">outgroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1609"></a><tt class="py-lineno">1609</tt>  <tt class="py-line">     </tt>
<a name="L1610"></a><tt class="py-lineno">1610</tt>  <tt class="py-line">            <tt class="py-comment"># These are all the requirements to apply the ancestral correction.</tt> </tt>
<a name="L1611"></a><tt class="py-lineno">1611</tt>  <tt class="py-line">            <tt class="py-comment"># First 2 are constant context.</tt> </tt>
<a name="L1612"></a><tt class="py-lineno">1612</tt>  <tt class="py-line">            <tt class="py-comment"># Next 2 are sensible context.</tt> </tt>
<a name="L1613"></a><tt class="py-lineno">1613</tt>  <tt class="py-line">            <tt class="py-comment"># Next 1 is that outgroup allele is one of the segregating.</tt> </tt>
<a name="L1614"></a><tt class="py-lineno">1614</tt>  <tt class="py-line">            <tt class="py-comment"># Next 2 are that segregating alleles are sensible.</tt> </tt>
<a name="L1615"></a><tt class="py-lineno">1615</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">outgroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-name">ingroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1616"></a><tt class="py-lineno">1616</tt>  <tt class="py-line">               <tt class="py-keyword">or</tt> <tt class="py-name">outgroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-name">ingroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1617"></a><tt class="py-lineno">1617</tt>  <tt class="py-line">               <tt class="py-keyword">or</tt> <tt class="py-name">ingroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">genetic_bases</tt>\ </tt>
<a name="L1618"></a><tt class="py-lineno">1618</tt>  <tt class="py-line">               <tt class="py-keyword">or</tt> <tt class="py-name">ingroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">genetic_bases</tt>\ </tt>
<a name="L1619"></a><tt class="py-lineno">1619</tt>  <tt class="py-line">               <tt class="py-keyword">or</tt> <tt class="py-name">outgroup_allele</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-name">allele1</tt><tt class="py-op">,</tt> <tt class="py-name">allele2</tt><tt class="py-op">]</tt>\ </tt>
<a name="L1620"></a><tt class="py-lineno">1620</tt>  <tt class="py-line">               <tt class="py-keyword">or</tt> <tt class="py-name">allele1</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">genetic_bases</tt>\ </tt>
<a name="L1621"></a><tt class="py-lineno">1621</tt>  <tt class="py-line">               <tt class="py-keyword">or</tt> <tt class="py-name">allele2</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">genetic_bases</tt><tt class="py-op">:</tt> </tt>
<a name="L1622"></a><tt class="py-lineno">1622</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L1623"></a><tt class="py-lineno">1623</tt>  <tt class="py-line">     </tt>
<a name="L1624"></a><tt class="py-lineno">1624</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">allele1</tt> <tt class="py-op">==</tt> <tt class="py-name">outgroup_allele</tt><tt class="py-op">:</tt> </tt>
<a name="L1625"></a><tt class="py-lineno">1625</tt>  <tt class="py-line">                <tt class="py-name">derived_allele</tt> <tt class="py-op">=</tt> <tt class="py-name">allele2</tt> </tt>
<a name="L1626"></a><tt class="py-lineno">1626</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt class="py-name">allele2</tt> <tt class="py-op">==</tt> <tt class="py-name">outgroup_allele</tt><tt class="py-op">:</tt> </tt>
<a name="L1627"></a><tt class="py-lineno">1627</tt>  <tt class="py-line">                <tt class="py-comment"># In this case, the second allele is non_outgroup</tt> </tt>
<a name="L1628"></a><tt class="py-lineno">1628</tt>  <tt class="py-line">                <tt class="py-name">derived_allele</tt> <tt class="py-op">=</tt> <tt class="py-name">allele1</tt> </tt>
<a name="L1629"></a><tt class="py-lineno">1629</tt>  <tt class="py-line">            <tt class="py-name">derived_tri</tt> <tt class="py-op">=</tt> <tt class="py-name">ingroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">derived_allele</tt> <tt class="py-op">+</tt> <tt class="py-name">ingroup_tri</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L1630"></a><tt class="py-lineno">1630</tt>  <tt class="py-line">            <tt class="py-name">result</tt><tt class="py-op">.</tt><tt class="py-name">setdefault</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">derived_tri</tt><tt class="py-op">,</tt> <tt class="py-name">outgroup_allele</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L1631"></a><tt class="py-lineno">1631</tt>  <tt class="py-line">            <tt class="py-name">result</tt><tt class="py-op">[</tt><tt class="py-name">derived_tri</tt><tt class="py-op">,</tt> <tt class="py-name">outgroup_allele</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">snp</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">snp_info</tt> </tt>
<a name="L1632"></a><tt class="py-lineno">1632</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
</div><a name="L1633"></a><tt class="py-lineno">1633</tt>  <tt class="py-line">     </tt>
<a name="L1634"></a><tt class="py-lineno">1634</tt>  <tt class="py-line">    <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="Spectrum.from_data_dict_corrected"></a><div id="Spectrum.from_data_dict_corrected-def"><a name="L1635"></a><tt class="py-lineno">1635</tt> <a class="py-toggle" href="#" id="Spectrum.from_data_dict_corrected-toggle" onclick="return toggle('Spectrum.from_data_dict_corrected');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#from_data_dict_corrected">from_data_dict_corrected</a><tt class="py-op">(</tt><tt class="py-param">data_dict</tt><tt class="py-op">,</tt> <tt class="py-param">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-param">projections</tt><tt class="py-op">,</tt> </tt>
<a name="L1636"></a><tt class="py-lineno">1636</tt>  <tt class="py-line">                                 <tt class="py-param">fux_filename</tt><tt class="py-op">,</tt> <tt class="py-param">force_pos</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> </tt>
<a name="L1637"></a><tt class="py-lineno">1637</tt>  <tt class="py-line">                                 <tt class="py-param">mask_corners</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum.from_data_dict_corrected-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum.from_data_dict_corrected-expanded"><a name="L1638"></a><tt class="py-lineno">1638</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1639"></a><tt class="py-lineno">1639</tt>  <tt class="py-line"><tt class="py-docstring">        Spectrum from a dictionary of polymorphisms, corrected for ancestral</tt> </tt>
<a name="L1640"></a><tt class="py-lineno">1640</tt>  <tt class="py-line"><tt class="py-docstring">        misidentification.</tt> </tt>
<a name="L1641"></a><tt class="py-lineno">1641</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1642"></a><tt class="py-lineno">1642</tt>  <tt class="py-line"><tt class="py-docstring">        The correction is based upon:</tt> </tt>
<a name="L1643"></a><tt class="py-lineno">1643</tt>  <tt class="py-line"><tt class="py-docstring">            Hernandez, Williamson &amp; Bustamante _Mol_Biol_Evol_ 24:1792 (2007)</tt> </tt>
<a name="L1644"></a><tt class="py-lineno">1644</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1645"></a><tt class="py-lineno">1645</tt>  <tt class="py-line"><tt class="py-docstring">        force_pos: If the correction is too agressive, it may leave some small</tt> </tt>
<a name="L1646"></a><tt class="py-lineno">1646</tt>  <tt class="py-line"><tt class="py-docstring">                   entries in the fs less than zero. If force_pos is true,</tt> </tt>
<a name="L1647"></a><tt class="py-lineno">1647</tt>  <tt class="py-line"><tt class="py-docstring">                   these entries will be set to zero, in such a way that the</tt> </tt>
<a name="L1648"></a><tt class="py-lineno">1648</tt>  <tt class="py-line"><tt class="py-docstring">                   total number of segregating SNPs is conserved.</tt> </tt>
<a name="L1649"></a><tt class="py-lineno">1649</tt>  <tt class="py-line"><tt class="py-docstring">        fux_filename: The name of the file containing the </tt> </tt>
<a name="L1650"></a><tt class="py-lineno">1650</tt>  <tt class="py-line"><tt class="py-docstring">                   misidentification probabilities.</tt> </tt>
<a name="L1651"></a><tt class="py-lineno">1651</tt>  <tt class="py-line"><tt class="py-docstring">                   The file is of the form:</tt> </tt>
<a name="L1652"></a><tt class="py-lineno">1652</tt>  <tt class="py-line"><tt class="py-docstring">                       # Any number of comments lines beginning with #</tt> </tt>
<a name="L1653"></a><tt class="py-lineno">1653</tt>  <tt class="py-line"><tt class="py-docstring">                       AAA T 0.001</tt> </tt>
<a name="L1654"></a><tt class="py-lineno">1654</tt>  <tt class="py-line"><tt class="py-docstring">                       AAA G 0.02</tt> </tt>
<a name="L1655"></a><tt class="py-lineno">1655</tt>  <tt class="py-line"><tt class="py-docstring">                       ...</tt> </tt>
<a name="L1656"></a><tt class="py-lineno">1656</tt>  <tt class="py-line"><tt class="py-docstring">                   Where every combination of three + one bases is considered</tt> </tt>
<a name="L1657"></a><tt class="py-lineno">1657</tt>  <tt class="py-line"><tt class="py-docstring">                   (order is not important).  The triplet is the context and</tt> </tt>
<a name="L1658"></a><tt class="py-lineno">1658</tt>  <tt class="py-line"><tt class="py-docstring">                   putatively derived allele (x) in the reference species. The</tt> </tt>
<a name="L1659"></a><tt class="py-lineno">1659</tt>  <tt class="py-line"><tt class="py-docstring">                   single base is the base (u) in the outgroup. The numerical</tt> </tt>
<a name="L1660"></a><tt class="py-lineno">1660</tt>  <tt class="py-line"><tt class="py-docstring">                   value is 1-f_{ux} in the notation of the paper.</tt> </tt>
<a name="L1661"></a><tt class="py-lineno">1661</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1662"></a><tt class="py-lineno">1662</tt>  <tt class="py-line"><tt class="py-docstring">        The data dictionary should be organized as:</tt> </tt>
<a name="L1663"></a><tt class="py-lineno">1663</tt>  <tt class="py-line"><tt class="py-docstring">            {snp_id:{'segregating': ['A','T'],</tt> </tt>
<a name="L1664"></a><tt class="py-lineno">1664</tt>  <tt class="py-line"><tt class="py-docstring">                     'calls': {'YRI': (23,3),</tt> </tt>
<a name="L1665"></a><tt class="py-lineno">1665</tt>  <tt class="py-line"><tt class="py-docstring">                                'CEU': (7,3)</tt> </tt>
<a name="L1666"></a><tt class="py-lineno">1666</tt>  <tt class="py-line"><tt class="py-docstring">                                },</tt> </tt>
<a name="L1667"></a><tt class="py-lineno">1667</tt>  <tt class="py-line"><tt class="py-docstring">                     'outgroup_allele': 'T',</tt> </tt>
<a name="L1668"></a><tt class="py-lineno">1668</tt>  <tt class="py-line"><tt class="py-docstring">                     'context': 'CAT',</tt> </tt>
<a name="L1669"></a><tt class="py-lineno">1669</tt>  <tt class="py-line"><tt class="py-docstring">                     'outgroup_context': 'CAT'</tt> </tt>
<a name="L1670"></a><tt class="py-lineno">1670</tt>  <tt class="py-line"><tt class="py-docstring">                    }</tt> </tt>
<a name="L1671"></a><tt class="py-lineno">1671</tt>  <tt class="py-line"><tt class="py-docstring">            }</tt> </tt>
<a name="L1672"></a><tt class="py-lineno">1672</tt>  <tt class="py-line"><tt class="py-docstring">        The additional entries are 'context', which includes the two flanking</tt> </tt>
<a name="L1673"></a><tt class="py-lineno">1673</tt>  <tt class="py-line"><tt class="py-docstring">        bases in the species of interest, and 'outgroup_context', which</tt> </tt>
<a name="L1674"></a><tt class="py-lineno">1674</tt>  <tt class="py-line"><tt class="py-docstring">        includes the aligned bases in the outgroup.</tt> </tt>
<a name="L1675"></a><tt class="py-lineno">1675</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L1676"></a><tt class="py-lineno">1676</tt>  <tt class="py-line"><tt class="py-docstring">        This method skips entries for which the correction cannot be applied.</tt> </tt>
<a name="L1677"></a><tt class="py-lineno">1677</tt>  <tt class="py-line"><tt class="py-docstring">        Most commonly this is because of missing or non-constant context.</tt> </tt>
<a name="L1678"></a><tt class="py-lineno">1678</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1679"></a><tt class="py-lineno">1679</tt>  <tt class="py-line">        <tt class="py-comment"># Read the fux file into a dictionary.</tt> </tt>
<a name="L1680"></a><tt class="py-lineno">1680</tt>  <tt class="py-line">        <tt class="py-name">fux_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L1681"></a><tt class="py-lineno">1681</tt>  <tt class="py-line">        <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">(</tt><tt class="py-name">fux_filename</tt><tt class="py-op">)</tt> </tt>
<a name="L1682"></a><tt class="py-lineno">1682</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">readlines</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1683"></a><tt class="py-lineno">1683</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'#'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L1684"></a><tt class="py-lineno">1684</tt>  <tt class="py-line">                <tt class="py-keyword">continue</tt> </tt>
<a name="L1685"></a><tt class="py-lineno">1685</tt>  <tt class="py-line">            <tt class="py-name">sp</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1686"></a><tt class="py-lineno">1686</tt>  <tt class="py-line">            <tt class="py-name">fux_dict</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">sp</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">sp</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">sp</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L1687"></a><tt class="py-lineno">1687</tt>  <tt class="py-line">        <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1688"></a><tt class="py-lineno">1688</tt>  <tt class="py-line">     </tt>
<a name="L1689"></a><tt class="py-lineno">1689</tt>  <tt class="py-line">        <tt class="py-comment"># Divide the data into classes based on ('context', 'outgroup_allele')</tt> </tt>
<a name="L1690"></a><tt class="py-lineno">1690</tt>  <tt class="py-line">        <tt class="py-name">by_context</tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-176', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-177" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum._data_by_tri()=dadi.Spectrum_mod.Spectrum-class.html#_data_by_tri"><a title="dadi.Spectrum_mod.Spectrum._data_by_tri" class="py-name" href="#" onclick="return doclink('link-177', '_data_by_tri', 'link-177');">_data_by_tri</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dict</tt><tt class="py-op">)</tt> </tt>
<a name="L1691"></a><tt class="py-lineno">1691</tt>  <tt class="py-line">     </tt>
<a name="L1692"></a><tt class="py-lineno">1692</tt>  <tt class="py-line">        <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">zeros</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">projections</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1693"></a><tt class="py-lineno">1693</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">by_context</tt><tt class="py-op">:</tt> </tt>
<a name="L1694"></a><tt class="py-lineno">1694</tt>  <tt class="py-line">            <tt class="py-comment"># Each time through this loop, we eliminate two entries from the </tt> </tt>
<a name="L1695"></a><tt class="py-lineno">1695</tt>  <tt class="py-line">            <tt class="py-comment"># data dictionary. These correspond to one class and its</tt> </tt>
<a name="L1696"></a><tt class="py-lineno">1696</tt>  <tt class="py-line">            <tt class="py-comment"># corresponding misidentified class.</tt> </tt>
<a name="L1697"></a><tt class="py-lineno">1697</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-name">derived_tri</tt><tt class="py-op">,</tt> <tt class="py-name">out_base</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">nomis_data</tt> <tt class="py-op">=</tt> <tt class="py-name">by_context</tt><tt class="py-op">.</tt><tt class="py-name">popitem</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L1698"></a><tt class="py-lineno">1698</tt>  <tt class="py-line"> </tt>
<a name="L1699"></a><tt class="py-lineno">1699</tt>  <tt class="py-line">            <tt class="py-comment"># The corresponding bases if the ancestral state had been</tt> </tt>
<a name="L1700"></a><tt class="py-lineno">1700</tt>  <tt class="py-line">            <tt class="py-comment"># misidentifed.</tt> </tt>
<a name="L1701"></a><tt class="py-lineno">1701</tt>  <tt class="py-line">            <tt class="py-name">mis_out_base</tt> <tt class="py-op">=</tt> <tt class="py-name">derived_tri</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L1702"></a><tt class="py-lineno">1702</tt>  <tt class="py-line">            <tt class="py-name">mis_derived_tri</tt> <tt class="py-op">=</tt> <tt class="py-name">derived_tri</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">out_base</tt> <tt class="py-op">+</tt> <tt class="py-name">derived_tri</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L1703"></a><tt class="py-lineno">1703</tt>  <tt class="py-line">            <tt class="py-comment"># Get the data for that case. Note that we default to an empty</tt> </tt>
<a name="L1704"></a><tt class="py-lineno">1704</tt>  <tt class="py-line">            <tt class="py-comment"># dictionary if we don't have data for that class.</tt> </tt>
<a name="L1705"></a><tt class="py-lineno">1705</tt>  <tt class="py-line">            <tt class="py-name">mis_data</tt> <tt class="py-op">=</tt> <tt class="py-name">by_context</tt><tt class="py-op">.</tt><tt class="py-name">pop</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">mis_derived_tri</tt><tt class="py-op">,</tt> <tt class="py-name">mis_out_base</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L1706"></a><tt class="py-lineno">1706</tt>  <tt class="py-line">     </tt>
<a name="L1707"></a><tt class="py-lineno">1707</tt>  <tt class="py-line">            <tt class="py-name">fux</tt> <tt class="py-op">=</tt> <tt class="py-name">fux_dict</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">derived_tri</tt><tt class="py-op">,</tt> <tt class="py-name">out_base</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L1708"></a><tt class="py-lineno">1708</tt>  <tt class="py-line">            <tt class="py-name">fxu</tt> <tt class="py-op">=</tt> <tt class="py-name">fux_dict</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">mis_derived_tri</tt><tt class="py-op">,</tt> <tt class="py-name">mis_out_base</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L1709"></a><tt class="py-lineno">1709</tt>  <tt class="py-line">     </tt>
<a name="L1710"></a><tt class="py-lineno">1710</tt>  <tt class="py-line">            <tt class="py-comment"># Get the spectra for these two cases</tt> </tt>
<a name="L1711"></a><tt class="py-lineno">1711</tt>  <tt class="py-line">            <tt class="py-name">Nux</tt> <tt class="py-op">=</tt> <tt id="link-178" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-178', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-179" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum.from_data_dict()=dadi.Spectrum_mod.Spectrum-class.html#from_data_dict"><a title="dadi.Spectrum_mod.Spectrum.from_data_dict" class="py-name" href="#" onclick="return doclink('link-179', 'from_data_dict', 'link-179');">from_data_dict</a></tt><tt class="py-op">(</tt><tt class="py-name">nomis_data</tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-name">projections</tt><tt class="py-op">)</tt> </tt>
<a name="L1712"></a><tt class="py-lineno">1712</tt>  <tt class="py-line">            <tt class="py-name">Nxu</tt> <tt class="py-op">=</tt> <tt id="link-180" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-180', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_data_dict" class="py-name" href="#" onclick="return doclink('link-181', 'from_data_dict', 'link-179');">from_data_dict</a></tt><tt class="py-op">(</tt><tt class="py-name">mis_data</tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-name">projections</tt><tt class="py-op">)</tt> </tt>
<a name="L1713"></a><tt class="py-lineno">1713</tt>  <tt class="py-line">     </tt>
<a name="L1714"></a><tt class="py-lineno">1714</tt>  <tt class="py-line">            <tt class="py-comment"># Equations 5 &amp; 6 from the paper.</tt> </tt>
<a name="L1715"></a><tt class="py-lineno">1715</tt>  <tt class="py-line">            <tt class="py-name">Nxu_rev</tt> <tt class="py-op">=</tt> <tt id="link-182" class="py-name"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-182', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">(</tt><tt class="py-name">Nxu</tt><tt class="py-op">)</tt> </tt>
<a name="L1716"></a><tt class="py-lineno">1716</tt>  <tt class="py-line">            <tt class="py-name">Rux</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">fxu</tt><tt class="py-op">*</tt><tt class="py-name">Nux</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">fxu</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">Nxu_rev</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">fux</tt><tt class="py-op">+</tt><tt class="py-name">fxu</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L1717"></a><tt class="py-lineno">1717</tt>  <tt class="py-line">            <tt class="py-name">Rxu</tt> <tt class="py-op">=</tt> <tt id="link-183" class="py-name"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-183', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">fux</tt><tt class="py-op">*</tt><tt class="py-name">Nxu_rev</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">fux</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">Nux</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">fux</tt><tt class="py-op">+</tt><tt class="py-name">fxu</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L1718"></a><tt class="py-lineno">1718</tt>  <tt class="py-line">     </tt>
<a name="L1719"></a><tt class="py-lineno">1719</tt>  <tt class="py-line">            <tt class="py-name">fs</tt> <tt class="py-op">+=</tt> <tt class="py-name">Rux</tt> <tt class="py-op">+</tt> <tt class="py-name">Rxu</tt> </tt>
<a name="L1720"></a><tt class="py-lineno">1720</tt>  <tt class="py-line">     </tt>
<a name="L1721"></a><tt class="py-lineno">1721</tt>  <tt class="py-line">        <tt class="py-comment"># Here we take the negative entries, and flip them back, so they end up</tt> </tt>
<a name="L1722"></a><tt class="py-lineno">1722</tt>  <tt class="py-line">        <tt class="py-comment"># zero and the total number of SNPs is conserved.</tt> </tt>
<a name="L1723"></a><tt class="py-lineno">1723</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">force_pos</tt><tt class="py-op">:</tt> </tt>
<a name="L1724"></a><tt class="py-lineno">1724</tt>  <tt class="py-line">            <tt class="py-name">negative_entries</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">minimum</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">)</tt> </tt>
<a name="L1725"></a><tt class="py-lineno">1725</tt>  <tt class="py-line">            <tt class="py-name">fs</tt> <tt class="py-op">-=</tt> <tt class="py-name">negative_entries</tt> </tt>
<a name="L1726"></a><tt class="py-lineno">1726</tt>  <tt class="py-line">            <tt class="py-name">fs</tt> <tt class="py-op">+=</tt> <tt id="link-184" class="py-name"><a title="dadi.Numerics.reverse_array" class="py-name" href="#" onclick="return doclink('link-184', 'reverse_array', 'link-6');">reverse_array</a></tt><tt class="py-op">(</tt><tt class="py-name">negative_entries</tt><tt class="py-op">)</tt> </tt>
<a name="L1727"></a><tt class="py-lineno">1727</tt>  <tt class="py-line">     </tt>
<a name="L1728"></a><tt class="py-lineno">1728</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-185" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-185', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">,</tt> <tt id="link-186" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-186', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt id="link-187" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-187', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1729"></a><tt class="py-lineno">1729</tt>  <tt class="py-line"> </tt>
<a name="L1730"></a><tt class="py-lineno">1730</tt>  <tt class="py-line">    <tt class="py-comment"># The code below ensures that when I do arithmetic with Spectrum objects,</tt> </tt>
<a name="L1731"></a><tt class="py-lineno">1731</tt>  <tt class="py-line">    <tt class="py-comment"># it is not done between a folded and an unfolded array. If it is, I raise</tt> </tt>
<a name="L1732"></a><tt class="py-lineno">1732</tt>  <tt class="py-line">    <tt class="py-comment"># a ValueError.</tt> </tt>
<a name="L1733"></a><tt class="py-lineno">1733</tt>  <tt class="py-line"> </tt>
<a name="L1734"></a><tt class="py-lineno">1734</tt>  <tt class="py-line">    <tt class="py-comment"># While I'm at it, I'm also fixing the annoying behavior that if a1 and a2</tt> </tt>
<a name="L1735"></a><tt class="py-lineno">1735</tt>  <tt class="py-line">    <tt class="py-comment"># are masked arrays, and a3 = a1 + a2. Then wherever a1 or a2 was masked,</tt> </tt>
<a name="L1736"></a><tt class="py-lineno">1736</tt>  <tt class="py-line">    <tt class="py-comment"># a3.data ends up with the a1.data values, rather than a1.data + a2.data.</tt> </tt>
<a name="L1737"></a><tt class="py-lineno">1737</tt>  <tt class="py-line">    <tt class="py-comment"># Note that this fix doesn't work for operation by numpy.ma.exp and </tt> </tt>
<a name="L1738"></a><tt class="py-lineno">1738</tt>  <tt class="py-line">    <tt class="py-comment"># numpy.ma.log. Guess I can't have everything.</tt> </tt>
<a name="L1739"></a><tt class="py-lineno">1739</tt>  <tt class="py-line"> </tt>
<a name="L1740"></a><tt class="py-lineno">1740</tt>  <tt class="py-line">    <tt class="py-comment"># I'm using exec here to avoid copy-pasting a dozen boiler-plate functions.</tt> </tt>
<a name="L1741"></a><tt class="py-lineno">1741</tt>  <tt class="py-line">    <tt class="py-comment"># The calls to check_folding_equal ensure that we don't try to combine</tt> </tt>
<a name="L1742"></a><tt class="py-lineno">1742</tt>  <tt class="py-line">    <tt class="py-comment"># folded and unfolded Spectrum objects.</tt> </tt>
<a name="L1743"></a><tt class="py-lineno">1743</tt>  <tt class="py-line"> </tt>
<a name="L1744"></a><tt class="py-lineno">1744</tt>  <tt class="py-line">    <tt class="py-comment"># I set check_folding = False in the constructor because it raises useless</tt> </tt>
<a name="L1745"></a><tt class="py-lineno">1745</tt>  <tt class="py-line">    <tt class="py-comment"># warnings when, for example, I do (model + 1). </tt> </tt>
<a name="L1746"></a><tt class="py-lineno">1746</tt>  <tt class="py-line"> </tt>
<a name="L1747"></a><tt class="py-lineno">1747</tt>  <tt class="py-line">    <tt class="py-comment"># These functions also ensure that the pop_ids and extrap_x attributes</tt> </tt>
<a name="L1748"></a><tt class="py-lineno">1748</tt>  <tt class="py-line">    <tt class="py-comment"># get properly copied over.</tt> </tt>
<a name="L1749"></a><tt class="py-lineno">1749</tt>  <tt class="py-line"> </tt>
<a name="L1750"></a><tt class="py-lineno">1750</tt>  <tt class="py-line">    <tt class="py-comment"># This is pretty advanced Python voodoo, so don't fret if you don't</tt> </tt>
<a name="L1751"></a><tt class="py-lineno">1751</tt>  <tt class="py-line">    <tt class="py-comment"># understand it at first glance. :-)</tt> </tt>
<a name="L1752"></a><tt class="py-lineno">1752</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">method</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">'__add__'</tt><tt class="py-op">,</tt><tt class="py-string">'__radd__'</tt><tt class="py-op">,</tt><tt class="py-string">'__sub__'</tt><tt class="py-op">,</tt><tt class="py-string">'__rsub__'</tt><tt class="py-op">,</tt><tt class="py-string">'__mul__'</tt><tt class="py-op">,</tt> </tt>
<a name="L1753"></a><tt class="py-lineno">1753</tt>  <tt class="py-line">                   <tt class="py-string">'__rmul__'</tt><tt class="py-op">,</tt><tt class="py-string">'__div__'</tt><tt class="py-op">,</tt><tt class="py-string">'__rdiv__'</tt><tt class="py-op">,</tt><tt class="py-string">'__truediv__'</tt><tt class="py-op">,</tt><tt class="py-string">'__rtruediv__'</tt><tt class="py-op">,</tt> </tt>
<a name="L1754"></a><tt class="py-lineno">1754</tt>  <tt class="py-line">                   <tt class="py-string">'__floordiv__'</tt><tt class="py-op">,</tt><tt class="py-string">'__rfloordiv__'</tt><tt class="py-op">,</tt><tt class="py-string">'__rpow__'</tt><tt class="py-op">,</tt><tt class="py-string">'__pow__'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1755"></a><tt class="py-lineno">1755</tt>  <tt class="py-line">        <tt class="py-keyword">exec</tt><tt class="py-op">(</tt><tt class="py-string">"""</tt> </tt>
<a name="L1756"></a><tt class="py-lineno">1756</tt>  <tt class="py-line"><tt class="py-string">def %(method)s(self, other):</tt> </tt>
<a name="L1757"></a><tt class="py-lineno">1757</tt>  <tt class="py-line"><tt class="py-string">    self._check_other_folding(other)</tt> </tt>
<a name="L1758"></a><tt class="py-lineno">1758</tt>  <tt class="py-line"><tt class="py-string">    if isinstance(other, numpy.ma.masked_array):</tt> </tt>
<a name="L1759"></a><tt class="py-lineno">1759</tt>  <tt class="py-line"><tt class="py-string">        newdata = self.data.%(method)s (other.data)</tt> </tt>
<a name="L1760"></a><tt class="py-lineno">1760</tt>  <tt class="py-line"><tt class="py-string">        newmask = numpy.ma.mask_or(self.mask, other.mask)</tt> </tt>
<a name="L1761"></a><tt class="py-lineno">1761</tt>  <tt class="py-line"><tt class="py-string">    else:</tt> </tt>
<a name="L1762"></a><tt class="py-lineno">1762</tt>  <tt class="py-line"><tt class="py-string">        newdata = self.data.%(method)s (other)</tt> </tt>
<a name="L1763"></a><tt class="py-lineno">1763</tt>  <tt class="py-line"><tt class="py-string">        newmask = self.mask</tt> </tt>
<a name="L1764"></a><tt class="py-lineno">1764</tt>  <tt class="py-line"><tt class="py-string">    newpop_ids = self.pop_ids</tt> </tt>
<a name="L1765"></a><tt class="py-lineno">1765</tt>  <tt class="py-line"><tt class="py-string">    if hasattr(other, 'pop_ids'):</tt> </tt>
<a name="L1766"></a><tt class="py-lineno">1766</tt>  <tt class="py-line"><tt class="py-string">        if other.pop_ids is None:</tt> </tt>
<a name="L1767"></a><tt class="py-lineno">1767</tt>  <tt class="py-line"><tt class="py-string">            newpop_ids = self.pop_ids</tt> </tt>
<a name="L1768"></a><tt class="py-lineno">1768</tt>  <tt class="py-line"><tt class="py-string">        elif self.pop_ids is None:</tt> </tt>
<a name="L1769"></a><tt class="py-lineno">1769</tt>  <tt class="py-line"><tt class="py-string">            newpop_ids = other.pop_ids</tt> </tt>
<a name="L1770"></a><tt class="py-lineno">1770</tt>  <tt class="py-line"><tt class="py-string">        elif other.pop_ids != self.pop_ids:</tt> </tt>
<a name="L1771"></a><tt class="py-lineno">1771</tt>  <tt class="py-line"><tt class="py-string">            logger.warn('Arithmetic between Spectra with different pop_ids. '</tt> </tt>
<a name="L1772"></a><tt class="py-lineno">1772</tt>  <tt class="py-line"><tt class="py-string">                        'Resulting pop_id may not be correct.')</tt> </tt>
<a name="L1773"></a><tt class="py-lineno">1773</tt>  <tt class="py-line"><tt class="py-string">    if hasattr(other, 'extrap_x') and self.extrap_x != other.extrap_x:</tt> </tt>
<a name="L1774"></a><tt class="py-lineno">1774</tt>  <tt class="py-line"><tt class="py-string">        extrap_x = None</tt> </tt>
<a name="L1775"></a><tt class="py-lineno">1775</tt>  <tt class="py-line"><tt class="py-string">    else:</tt> </tt>
<a name="L1776"></a><tt class="py-lineno">1776</tt>  <tt class="py-line"><tt class="py-string">        extrap_x = self.extrap_x</tt> </tt>
<a name="L1777"></a><tt class="py-lineno">1777</tt>  <tt class="py-line"><tt class="py-string">    outfs = self.__class__.__new__(self.__class__, newdata, newmask, </tt> </tt>
<a name="L1778"></a><tt class="py-lineno">1778</tt>  <tt class="py-line"><tt class="py-string">                                   mask_corners=False, data_folded=self.folded,</tt> </tt>
<a name="L1779"></a><tt class="py-lineno">1779</tt>  <tt class="py-line"><tt class="py-string">                                   check_folding=False, pop_ids=newpop_ids,</tt> </tt>
<a name="L1780"></a><tt class="py-lineno">1780</tt>  <tt class="py-line"><tt class="py-string">                                   extrap_x=extrap_x)</tt> </tt>
<a name="L1781"></a><tt class="py-lineno">1781</tt>  <tt class="py-line"><tt class="py-string">    return outfs</tt> </tt>
<a name="L1782"></a><tt class="py-lineno">1782</tt>  <tt class="py-line"><tt class="py-string">"""</tt> <tt class="py-op">%</tt> <tt class="py-op">{</tt><tt class="py-string">'method'</tt><tt class="py-op">:</tt><tt class="py-name">method</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L1783"></a><tt class="py-lineno">1783</tt>  <tt class="py-line"> </tt>
<a name="L1784"></a><tt class="py-lineno">1784</tt>  <tt class="py-line">    <tt class="py-comment"># Methods that modify the Spectrum in-place.</tt> </tt>
<a name="L1785"></a><tt class="py-lineno">1785</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">method</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">'__iadd__'</tt><tt class="py-op">,</tt><tt class="py-string">'__isub__'</tt><tt class="py-op">,</tt><tt class="py-string">'__imul__'</tt><tt class="py-op">,</tt><tt class="py-string">'__idiv__'</tt><tt class="py-op">,</tt> </tt>
<a name="L1786"></a><tt class="py-lineno">1786</tt>  <tt class="py-line">                   <tt class="py-string">'__itruediv__'</tt><tt class="py-op">,</tt><tt class="py-string">'__ifloordiv__'</tt><tt class="py-op">,</tt><tt class="py-string">'__ipow__'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L1787"></a><tt class="py-lineno">1787</tt>  <tt class="py-line">        <tt class="py-keyword">exec</tt><tt class="py-op">(</tt><tt class="py-string">"""</tt> </tt>
<a name="L1788"></a><tt class="py-lineno">1788</tt>  <tt class="py-line"><tt class="py-string">def %(method)s(self, other):</tt> </tt>
<a name="L1789"></a><tt class="py-lineno">1789</tt>  <tt class="py-line"><tt class="py-string">    self._check_other_folding(other)</tt> </tt>
<a name="L1790"></a><tt class="py-lineno">1790</tt>  <tt class="py-line"><tt class="py-string">    if isinstance(other, numpy.ma.masked_array):</tt> </tt>
<a name="L1791"></a><tt class="py-lineno">1791</tt>  <tt class="py-line"><tt class="py-string">        self.data.%(method)s (other.data)</tt> </tt>
<a name="L1792"></a><tt class="py-lineno">1792</tt>  <tt class="py-line"><tt class="py-string">        self.mask = numpy.ma.mask_or(self.mask, other.mask)</tt> </tt>
<a name="L1793"></a><tt class="py-lineno">1793</tt>  <tt class="py-line"><tt class="py-string">    else:</tt> </tt>
<a name="L1794"></a><tt class="py-lineno">1794</tt>  <tt class="py-line"><tt class="py-string">        self.data.%(method)s (other)</tt> </tt>
<a name="L1795"></a><tt class="py-lineno">1795</tt>  <tt class="py-line"><tt class="py-string">    if hasattr(other, 'pop_ids') and other.pop_ids is not None\</tt> </tt>
<a name="L1796"></a><tt class="py-lineno">1796</tt>  <tt class="py-line"><tt class="py-string">             and other.pop_ids != self.pop_ids:</tt> </tt>
<a name="L1797"></a><tt class="py-lineno">1797</tt>  <tt class="py-line"><tt class="py-string">        logger.warn('Arithmetic between Spectra with different pop_ids. '</tt> </tt>
<a name="L1798"></a><tt class="py-lineno">1798</tt>  <tt class="py-line"><tt class="py-string">                    'Resulting pop_id may not be correct.')</tt> </tt>
<a name="L1799"></a><tt class="py-lineno">1799</tt>  <tt class="py-line"><tt class="py-string">    if hasattr(other, 'extrap_x') and self.extrap_x != other.extrap_x:</tt> </tt>
<a name="L1800"></a><tt class="py-lineno">1800</tt>  <tt class="py-line"><tt class="py-string">        self.extrap_x = None</tt> </tt>
<a name="L1801"></a><tt class="py-lineno">1801</tt>  <tt class="py-line"><tt class="py-string">    return self</tt> </tt>
<a name="L1802"></a><tt class="py-lineno">1802</tt>  <tt class="py-line"><tt class="py-string">"""</tt> <tt class="py-op">%</tt> <tt class="py-op">{</tt><tt class="py-string">'method'</tt><tt class="py-op">:</tt><tt class="py-name">method</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L1803"></a><tt class="py-lineno">1803</tt>  <tt class="py-line"> </tt>
<a name="Spectrum._check_other_folding"></a><div id="Spectrum._check_other_folding-def"><a name="L1804"></a><tt class="py-lineno">1804</tt> <a class="py-toggle" href="#" id="Spectrum._check_other_folding-toggle" onclick="return toggle('Spectrum._check_other_folding');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod.Spectrum-class.html#_check_other_folding">_check_other_folding</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum._check_other_folding-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="Spectrum._check_other_folding-expanded"><a name="L1805"></a><tt class="py-lineno">1805</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L1806"></a><tt class="py-lineno">1806</tt>  <tt class="py-line"><tt class="py-docstring">        Ensure other Spectrum has same .folded status</tt> </tt>
<a name="L1807"></a><tt class="py-lineno">1807</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L1808"></a><tt class="py-lineno">1808</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">)</tt>\ </tt>
<a name="L1809"></a><tt class="py-lineno">1809</tt>  <tt class="py-line">           <tt class="py-keyword">and</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt> <tt class="py-op">!=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">:</tt> </tt>
<a name="L1810"></a><tt class="py-lineno">1810</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">'Cannot operate with a folded Spectrum and an '</tt> </tt>
<a name="L1811"></a><tt class="py-lineno">1811</tt>  <tt class="py-line">                             <tt class="py-string">'unfolded one.'</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L1812"></a><tt class="py-lineno">1812</tt>  <tt class="py-line"> </tt>
<a name="L1813"></a><tt class="py-lineno">1813</tt>  <tt class="py-line"><tt class="py-comment"># Allow spectrum objects to be pickled. </tt> </tt>
<a name="L1814"></a><tt class="py-lineno">1814</tt>  <tt class="py-line"><tt class="py-comment"># See http://effbot.org/librarybook/copy-reg.htm</tt> </tt>
<a name="L1815"></a><tt class="py-lineno">1815</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">copy_reg</tt> </tt>
<a name="Spectrum_unpickler"></a><div id="Spectrum_unpickler-def"><a name="L1816"></a><tt class="py-lineno">1816</tt> <a class="py-toggle" href="#" id="Spectrum_unpickler-toggle" onclick="return toggle('Spectrum_unpickler');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod-module.html#Spectrum_unpickler">Spectrum_unpickler</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">mask</tt><tt class="py-op">,</tt> <tt class="py-param">data_folded</tt><tt class="py-op">,</tt> <tt class="py-param">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-param">extrap_x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum_unpickler-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="Spectrum_unpickler-expanded"><a name="L1817"></a><tt class="py-lineno">1817</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-188" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-188', 'dadi', 'link-2');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-189', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">mask</tt><tt class="py-op">,</tt> <tt id="link-190" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-190', 'mask_corners', 'link-14');">mask_corners</a></tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-name">data_folded</tt><tt class="py-op">=</tt><tt class="py-name">data_folded</tt><tt class="py-op">,</tt> <tt class="py-name">check_folding</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-name">pop_ids</tt><tt class="py-op">=</tt><tt class="py-name">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-name">extrap_x</tt><tt class="py-op">=</tt><tt class="py-name">extrap_x</tt><tt class="py-op">)</tt> </tt>
</div><a name="Spectrum_pickler"></a><div id="Spectrum_pickler-def"><a name="L1818"></a><tt class="py-lineno">1818</tt> <a class="py-toggle" href="#" id="Spectrum_pickler-toggle" onclick="return toggle('Spectrum_pickler');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Spectrum_mod-module.html#Spectrum_pickler">Spectrum_pickler</a><tt class="py-op">(</tt><tt class="py-param">fs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Spectrum_pickler-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="Spectrum_pickler-expanded"><a name="L1819"></a><tt class="py-lineno">1819</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">Spectrum_unpickler</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">folded</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">pop_ids</tt><tt class="py-op">,</tt> <tt class="py-name">fs</tt><tt class="py-op">.</tt><tt class="py-name">extrap_x</tt><tt class="py-op">)</tt> </tt>
</div><a name="L1820"></a><tt class="py-lineno">1820</tt>  <tt class="py-line"><tt class="py-name">copy_reg</tt><tt class="py-op">.</tt><tt class="py-name">pickle</tt><tt class="py-op">(</tt><tt id="link-191" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-191', 'Spectrum', 'link-28');">Spectrum</a></tt><tt class="py-op">,</tt> <tt class="py-name">Spectrum_pickler</tt><tt class="py-op">,</tt> <tt class="py-name">Spectrum_unpickler</tt><tt class="py-op">)</tt> </tt>
<a name="L1821"></a><tt class="py-lineno">1821</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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